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Loading source files for package edu.yale.csgp.vitapad.util... Loading source files for package edu.yale.csgp.vitapad.util.geom... Loading source files for package edu.yale.csgp.vitapad.util.logging... Loading source files for package edu.yale.csgp.vitapad.util.texhyphj... Loading source files for package edu.yale.csgp.vitapad.util.xml... Loading source files for package edu.yale.csgp.vitapad.visual... Loading source files for package edu.yale.csgp.vitapad.visual.graphics... Loading source files for package edu.yale.csgp.vitapad.visual.paint... Loading source files for package edu.yale.csgp.vitapad.visual.type... Constructing Javadoc information... Standard Doclet version 1.5.0 Building tree for all the packages and classes... src\edu\yale\csgp\vitapad\EditPane.java:40: warning - Tag @see: reference not found: edu.yale.vitapad.MainFrame src\edu\yale\csgp\vitapad\EditPane.java:40: warning - Tag @see: reference not found: edu.yale.graph.visual.GraphScrollPane src\edu\yale\csgp\vitapad\EditPane.java:40: warning - Tag @see: reference not found: edu.yale.graph.visual.GraphToolBar src\edu\yale\csgp\vitapad\GraphPanel.java:91: warning - Tag @see: can't find setViewMode() in edu.yale.csgp.vitapad.GraphPanel src\edu\yale\csgp\vitapad\GraphPanel.java:91: warning - Tag @see: can't find setEditMode() in edu.yale.csgp.vitapad.GraphPanel src\edu\yale\csgp\vitapad\GraphPanel.java:91: warning - Tag @see: can't find setVertexMode() in edu.yale.csgp.vitapad.GraphPanel src\edu\yale\csgp\vitapad\GraphPanel.java:91: warning - Tag @see: can't find setEdgeMode() in edu.yale.csgp.vitapad.GraphPanel src\edu\yale\csgp\vitapad\GraphPanel.java:207: warning - 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@param argument "value" is not a parameter name. src\edu\yale\csgp\vitapad\GUIUtils.java:495: warning - @param argument "def" is not a parameter name. src\edu\yale\csgp\vitapad\graph\AbstractGraph.java:374: warning - @return tag has no arguments. src\edu\yale\csgp\vitapad\graph\DataClass.java:100: warning - @return tag has no arguments. src\edu\yale\csgp\vitapad\graph\DecorableElement.java:18: warning - Tag @see: reference not found: edu.yale.graph.DecorableElementImp src\edu\yale\csgp\vitapad\graph\DecorableElementImp.java:15: warning - Tag @see: reference not found: edu.yale.graph.DecorableElementImp src\edu\yale\csgp\vitapad\graph\DecorableElementImp.java:15: warning - Tag @see: reference not found: edu.yale.graph.Edge src\edu\yale\csgp\vitapad\graph\DecorableElementImp.java:162: warning - @return tag has no arguments. src\edu\yale\csgp\vitapad\graph\Decoration.java:22: warning - Tag @see: reference not found: edu.yale.graph.DecorationImp src\edu\yale\csgp\vitapad\graph\Decoration.java:22: warning - 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Tag @see: reference not found: edu.yale.graph.Link src\edu\yale\csgp\vitapad\graph\Edge.java:23: warning - Tag @see: reference not found: edu.yale.graph.visual.VisualEdge src\edu\yale\csgp\vitapad\graph\Experiment.java:69: warning - @return tag has no arguments. src\edu\yale\csgp\vitapad\graph\Experiment.java:77: warning - @return tag has no arguments. src\edu\yale\csgp\vitapad\graph\Experiment.java:85: warning - @return tag has no arguments. src\edu\yale\csgp\vitapad\graph\Experiment.java:93: warning - @return tag has no arguments. src\edu\yale\csgp\vitapad\graph\Experiment.java:109: warning - @param argument "string" is not a parameter name. src\edu\yale\csgp\vitapad\graph\Experiment.java:117: warning - @param argument "b" is not a parameter name. src\edu\yale\csgp\vitapad\graph\Graph.java:24: warning - Tag @see: reference not found: edu.yale.graph.GraphImp src\edu\yale\csgp\vitapad\graph\Graph.java:24: warning - Tag @see: reference not found: edu.yale.graph.visual.VisualGraph src\edu\yale\csgp\vitapad\graph\GraphElement.java:9: warning - Tag @see: reference not found: edu.yale.graph.visual.VisualGraphElement src\edu\yale\csgp\vitapad\graph\GraphEvent.java:13: warning - Tag @see: reference not found: edu.yale.graph.GraphListener src\edu\yale\csgp\vitapad\graph\GraphEvent.java:13: warning - Tag @see: reference not found: edu.yale.graph.DecorationListener src\edu\yale\csgp\vitapad\graph\GraphEvent.java:110: warning - @param argument "string" is not a parameter name. src\edu\yale\csgp\vitapad\graph\GraphListener.java:13: warning - Tag @see: reference not found: edu.yale.graph.visual.VisualGraph src\edu\yale\csgp\vitapad\graph\LabeledElement.java:10: warning - Tag @see: reference not found: edu.yale.graph.LabeledElementImp src\edu\yale\csgp\vitapad\graph\LabeledElementImp.java:8: warning - Tag @see: reference not found: edu.yale.graph.LabeledElement src\edu\yale\csgp\vitapad\graph\LinkableElement.java:12: warning - Tag @see: reference not found: edu.yale.graph.LinkableElementImp src\edu\yale\csgp\vitapad\graph\LinkableElement.java:37: warning - Tag @see: can't find setEnabled(boolean enabled) in edu.yale.csgp.vitapad.graph.LinkableElement src\edu\yale\csgp\vitapad\graph\LinkableElement.java:44: warning - Tag @see: can't find isEnabled() in edu.yale.csgp.vitapad.graph.LinkableElement src\edu\yale\csgp\vitapad\graph\LinkableElementImp.java:8: warning - Tag @see: reference not found: edu.yale.graph.LinkableElement src\edu\yale\csgp\vitapad\graph\LinkableElementImp.java:46: warning - Tag @see: can't find setEnabled(boolean enabled) in edu.yale.csgp.vitapad.graph.LinkableElementImp src\edu\yale\csgp\vitapad\graph\LinkableElementImp.java:56: warning - Tag @see: can't find isEnabled() in edu.yale.csgp.vitapad.graph.LinkableElementImp src\edu\yale\csgp\vitapad\graph\PathwayDecoration.java:29: warning - Tag @see: reference not found: edu.yale.graph.Decoration src\edu\yale\csgp\vitapad\graph\PathwayDecoration.java:29: warning - Tag @see: reference not found: edu.yale.graph.PWEnzyme src\edu\yale\csgp\vitapad\graph\PathwayDecoration.java:118: warning - @return tag has no arguments. src\edu\yale\csgp\vitapad\graph\PathwayDecoration.java:126: warning - @return tag has no arguments. src\edu\yale\csgp\vitapad\graph\PathwayDecoration.java:134: warning - @return tag has no arguments. src\edu\yale\csgp\vitapad\graph\PathwayDecoration.java:142: warning - @return tag has no arguments. src\edu\yale\csgp\vitapad\graph\PathwayDecoration.java:477: warning - @return tag has no arguments. src\edu\yale\csgp\vitapad\graph\PathwayDecoration.java:150: warning - @return tag has no arguments. src\edu\yale\csgp\vitapad\graph\TooltipElement.java:36: warning - Tag @see: can't find setEnabled(boolean enabled) in edu.yale.csgp.vitapad.graph.TooltipElement src\edu\yale\csgp\vitapad\graph\TooltipElement.java:43: warning - Tag @see: can't find isEnabled() in edu.yale.csgp.vitapad.graph.TooltipElement src\edu\yale\csgp\vitapad\graph\PathwayEdge.java:31: warning - Tag @see: reference not found: edu.yale.graph.Edge src\edu\yale\csgp\vitapad\graph\PathwayEdge.java:31: warning - Tag @see: reference not found: edu.yale.graph.Link src\edu\yale\csgp\vitapad\graph\PathwayEdge.java:348: warning - @return tag has no arguments. src\edu\yale\csgp\vitapad\graph\PathwayEdge.java:356: warning - @return tag has no arguments. src\edu\yale\csgp\vitapad\graph\PathwayEdge.java:366: warning - @return tag has no arguments. src\edu\yale\csgp\vitapad\graph\PathwayEdge.java:411: warning - @return tag has no arguments. src\edu\yale\csgp\vitapad\graph\PathwayEdge.java:366: warning - @param argument "edge" is not a parameter name. src\edu\yale\csgp\vitapad\graph\PathwayGraph.java:23: warning - Tag @see: reference not found: edu.yale.graph.Graph src\edu\yale\csgp\vitapad\graph\PathwayGraph.java:291: warning - @return tag has no arguments. src\edu\yale\csgp\vitapad\graph\PathwayGraph.java:283: warning - @return tag has no arguments. src\edu\yale\csgp\vitapad\graph\PathwayGraph.java:77: warning - @return tag has no arguments. src\edu\yale\csgp\vitapad\graph\PathwayGraph.java:85: warning - @param argument "pathway" is not a parameter name. src\edu\yale\csgp\vitapad\graph\PathwayGraph.java:265: warning - @param argument "exp" is not a parameter name. src\edu\yale\csgp\vitapad\graph\PathwayVertex.java:28: warning - Tag @see: reference not found: edu.yale.graph.Vertex src\edu\yale\csgp\vitapad\graph\PathwayVertex.java:28: warning - Tag @see: reference not found: edu.yale.graph.PWVertex src\edu\yale\csgp\vitapad\graph\PathwayVertex.java:155: warning - @return tag has no arguments. src\edu\yale\csgp\vitapad\graph\PathwayVertex.java:220: warning - @return tag has no arguments. src\edu\yale\csgp\vitapad\graph\PathwayVertex.java:228: warning - @return tag has no arguments. src\edu\yale\csgp\vitapad\graph\PathwayVertex.java:163: warning - @return tag has no arguments. src\edu\yale\csgp\vitapad\graph\PathwayVertex.java:462: warning - @return tag has no arguments. src\edu\yale\csgp\vitapad\graph\PathwayVertex.java:171: warning - @return tag has no arguments. src\edu\yale\csgp\vitapad\graph\PathwayVertex.java:179: warning - @return tag has no arguments. src\edu\yale\csgp\vitapad\graph\PathwayVertex.java:187: warning - @return tag has no arguments. src\edu\yale\csgp\vitapad\graph\PathwayVertex.java:244: warning - @param argument "i" is not a parameter name. src\edu\yale\csgp\vitapad\graph\TooltipElement.java:11: warning - Tag @see: reference not found: edu.yale.graph.ToolTippedElementImp src\edu\yale\csgp\vitapad\graph\TooltipElementImp.java:8: warning - Tag @see: reference not found: edu.yale.graph.ToolTippedElement src\edu\yale\csgp\vitapad\graph\TooltipElementImp.java:47: warning - Tag @see: can't find setEnabled(boolean enabled) in edu.yale.csgp.vitapad.graph.TooltipElementImp src\edu\yale\csgp\vitapad\graph\TooltipElementImp.java:57: warning - Tag @see: can't find isEnabled() in edu.yale.csgp.vitapad.graph.TooltipElementImp src\edu\yale\csgp\vitapad\graph\Vertex.java:20: warning - Tag @see: reference not found: edu.yale.graph.VertexImp src\edu\yale\csgp\vitapad\graph\Vertex.java:20: warning - Tag @see: reference not found: edu.yale.graph.PWVertex src\edu\yale\csgp\vitapad\graph\Vertex.java:20: warning - Tag @see: reference not found: edu.yale.graph.Compound src\edu\yale\csgp\vitapad\graph\Vertex.java:20: warning - Tag @see: reference not found: edu.yale.graph.visual.VisualVertex src\edu\yale\csgp\vitapad\graph\VPGradient.java:132: warning - @return tag has no arguments. src\edu\yale\csgp\vitapad\graph\VPGradient.java:141: warning - @return tag has no arguments. src\edu\yale\csgp\vitapad\graph\VPGradient.java:149: warning - @return tag has no arguments. src\edu\yale\csgp\vitapad\graph\VPGradient.java:157: warning - @return tag has no arguments. src\edu\yale\csgp\vitapad\graph\VPGradient.java:165: warning - @return tag has no arguments. src\edu\yale\csgp\vitapad\graph\VPGradient.java:173: warning - @return tag has no arguments. src\edu\yale\csgp\vitapad\graph\VPGradient.java:181: warning - @return tag has no arguments. src\edu\yale\csgp\vitapad\graph\VPGradient.java:197: warning - @param argument "d" is not a parameter name. src\edu\yale\csgp\vitapad\graph\VPGradient.java:221: warning - @param argument "d" is not a parameter name. src\edu\yale\csgp\vitapad\gui\components\AnnotationArea.java:145: warning - @return tag has no arguments. src\edu\yale\csgp\vitapad\gui\components\AnnotationArea.java:153: warning - @return tag has no arguments. src\edu\yale\csgp\vitapad\gui\components\AnnotationArea.java:161: warning - @param argument "i" is not a parameter name. src\edu\yale\csgp\vitapad\gui\components\AnnotationArea.java:169: warning - @param argument "i" is not a parameter name. src\edu\yale\csgp\vitapad\gui\components\ExpandableVPRLabel.java:54: warning - @param argument "i" is not a parameter name. src\edu\yale\csgp\vitapad\gui\components\GradientLabel.java:86: warning - @return tag has no arguments. src\edu\yale\csgp\vitapad\gui\components\GradientLabel.java:94: warning - @return tag has no arguments. src\edu\yale\csgp\vitapad\gui\components\GradientLabel.java:102: warning - @return tag has no arguments. src\edu\yale\csgp\vitapad\gui\components\GradientLabel.java:134: warning - @return tag has no arguments. src\edu\yale\csgp\vitapad\gui\components\TypeButton.java:289: warning - @return tag has no arguments. src\edu\yale\csgp\vitapad\gui\components\TypeButton.java:281: warning - @return tag has no arguments. src\edu\yale\csgp\vitapad\util\GlassPane.java:24: warning - @param argument "Container" is not a parameter name. src\edu\yale\csgp\vitapad\util\Resources.java:47: warning - @param argument "string" is not a parameter name. src\edu\yale\csgp\vitapad\util\geom\Geometry.java:143: warning - @return tag has no arguments. src\edu\yale\csgp\vitapad\util\texhyphj\Hyphenator.java:29: warning - Tag @see: reference not found: net.davidashen.util.ErrorHandler src\edu\yale\csgp\vitapad\util\texhyphj\List.java:325: warning - Tag @see: reference not found: net.davidashen.util.Applicator src\edu\yale\csgp\vitapad\util\texhyphj\List.java:342: warning - Tag @see: reference not found: net.davidashen.util.Applicator src\edu\yale\csgp\vitapad\visual\AbstractLabeledRenderer.java:20: warning - Tag @see: reference not found: edu.yale.graph.visual.LabeledVisualGraphElement src\edu\yale\csgp\vitapad\visual\AbstractLabeledRenderer.java:20: warning - Tag @see: reference not found: edu.yale.graph.visual.VisualVertex src\edu\yale\csgp\vitapad\visual\AbstractLabeledRenderer.java:20: warning - Tag @see: reference not found: edu.yale.graph.visual.VisualDecoration src\edu\yale\csgp\vitapad\visual\AbstractRenderer.java:29: warning - Tag @see: reference not found: edu.yale.graph.visual.VisualGraphElement src\edu\yale\csgp\vitapad\visual\AbstractRenderer.java:29: warning - Tag @see: reference not found: edu.yale.graph.visual.VisualVertex src\edu\yale\csgp\vitapad\visual\AbstractRenderer.java:29: warning - Tag @see: reference not found: edu.yale.graph.visual.VisualDecoration src\edu\yale\csgp\vitapad\visual\AbstractRenderer.java:29: warning - Tag @see: reference not found: edu.yale.graph.visual.VisualEdge src\edu\yale\csgp\vitapad\visual\AbstractRenderer.java:129: warning - Tag @see: can't find setTexturePaint() in edu.yale.csgp.vitapad.visual.AbstractRenderer src\edu\yale\csgp\vitapad\visual\EdgeRenderer.java:52: warning - @return tag has no arguments. src\edu\yale\csgp\vitapad\visual\EdgeRenderer.java:60: warning - @return tag has no arguments. src\edu\yale\csgp\vitapad\visual\LabeledRenderer.java:18: warning - Tag @see: reference not found: edu.yale.graph.visual.VisualGraphElement src\edu\yale\csgp\vitapad\visual\LabeledRenderer.java:18: warning - Tag @see: reference not found: edu.yale.graph.visual.VisualVertex src\edu\yale\csgp\vitapad\visual\LabeledRenderer.java:18: warning - Tag @see: reference not found: edu.yale.graph.visual.VisualDecoration src\edu\yale\csgp\vitapad\visual\Renderer.java:31: warning - Tag @see: reference not found: edu.yale.graph.GraphElement src\edu\yale\csgp\vitapad\visual\Renderer.java:31: warning - Tag @see: reference not found: edu.yale.graph.visual.LabeledVisualGraphElement src\edu\yale\csgp\vitapad\visual\Renderer.java:31: warning - Tag @see: reference not found: edu.yale.graph.visual.AbstractVisualGraphElement src\edu\yale\csgp\vitapad\visual\Renderer.java:31: warning - Tag @see: reference not found: edu.yale.graph.visual.VisualEdge src\edu\yale\csgp\vitapad\visual\Renderer.java:31: warning - Tag @see: reference not found: edu.yale.graph.visual.VisualVertex src\edu\yale\csgp\vitapad\visual\Renderer.java:31: warning - Tag @see: reference not found: edu.yale.graph.visual.VisualDecoration src\edu\yale\csgp\vitapad\visual\VertexRenderer.java:75: warning - @return tag has no arguments. src\edu\yale\csgp\vitapad\visual\paint\DecorationPainterFactory.java:11: warning - Tag @see: reference not found: edu.yale.graph.visual.painting.VisualDecorationPainterFactoryImp src\edu\yale\csgp\vitapad\visual\paint\DecorationPainterFactoryImp.java:11: warning - Tag @see: reference not found: edu.yale.graph.visual.painting.VisualVertexPainterImp src\edu\yale\csgp\vitapad\visual\paint\EdgePainter.java:12: warning - Tag @see: reference not found: edu.yale.graph.visual.painting.VisualEdgePainterImp src\edu\yale\csgp\vitapad\visual\paint\EdgePainterFactory.java:11: warning - Tag @see: reference not found: edu.yale.graph.visual.painting.VisualEdgePainterFactoryImp src\edu\yale\csgp\vitapad\visual\paint\EdgePainterFactoryImp.java:11: warning - Tag @see: reference not found: edu.yale.graph.visual.painting.VisualEdgePainterImp src\edu\yale\csgp\vitapad\visual\paint\Painter.java:13: warning - Tag @see: reference not found: edu.yale.graph.visual.painting.PainterFactory src\edu\yale\csgp\vitapad\visual\paint\PainterFactory.java:10: warning - Tag @see: reference not found: edu.yale.graph.visual.painting.Painter src\edu\yale\csgp\vitapad\visual\paint\VertexPainter.java:13: warning - Tag @see: reference not found: edu.yale.graph.visual.painting.VisualVertexPainterImp src\edu\yale\csgp\vitapad\visual\paint\VertexPainterFactory.java:11: warning - Tag @see: reference not found: edu.yale.graph.visual.painting.VisualVertexPainterFactoryImp src\edu\yale\csgp\vitapad\visual\paint\VertexPainterFactoryImp.java:11: warning - Tag @see: reference not found: edu.yale.graph.visual.painting.VisualVertexPainterImp src\edu\yale\csgp\vitapad\visual\paint\VertexPainterImp.java:20: warning - Tag @see: reference not found: edu.yale.graph.visual.painting.VisualVertexPainter src\edu\yale\csgp\vitapad\visual\type\InvisibleVertex.java:13: warning - Tag @see: reference not found: edu.yale.graph.DummyVertex src\edu\yale\csgp\vitapad\visual\type\Type.java:27: warning - Tag @see: reference not found: edu.yale.graph.type.TypeImp src\edu\yale\csgp\vitapad\visual\type\Type.java:27: warning - Tag @see: reference not found: edu.yale.graph.type.DefaultVertexType1 src\edu\yale\csgp\vitapad\visual\type\Type.java:27: warning - Tag @see: reference not found: edu.yale.graph.type.DefaultVertexType2 src\edu\yale\csgp\vitapad\visual\type\Type.java:27: warning - Tag @see: reference not found: edu.yale.graph.type.DefaultEdgeType1 src\edu\yale\csgp\vitapad\visual\type\Type.java:27: warning - Tag @see: reference not found: edu.yale.graph.type.DefaultEdgeType2 src\edu\yale\csgp\vitapad\visual\type\Type.java:27: warning - Tag @see: reference not found: edu.yale.graph.type.DefaultDecorationType1 src\edu\yale\csgp\vitapad\visual\type\Type.java:27: warning - Tag @see: reference not found: edu.yale.graph.type.DefaultDecorationType2 src\edu\yale\csgp\vitapad\visual\type\Type.java:27: warning - Tag @see: reference not found: edu.yale.graph.type.InvisibleVertex src\edu\yale\csgp\vitapad\visual\type\Type.java:222: warning - Tag @see: can't find setShortName(String shortName) in edu.yale.csgp.vitapad.visual.type.Type src\edu\yale\csgp\vitapad\visual\type\Type.java:356: warning - Tag @see: can't find getShortName() in edu.yale.csgp.vitapad.visual.type.Type src\edu\yale\csgp\vitapad\visual\type\Type.java:119: warning - @param argument "curvature" is not a parameter name. src\edu\yale\csgp\vitapad\gui\dialogs\CompoundDisplayPanel.java:57: warning - Tag @author cannot be used in field documentation. It can only be used in the following types of documentation: overview, package, class/interface. Generating target\docs\apidocs\serialized-form.html... Copying file C:\Documents and Settings\Matt Holford\.maven\cache\maven-javadoc-plugin-1.7\plugin-resources\stylesheet.css to file target\docs\apidocs\stylesheet.css... src\edu\yale\csgp\vitapad\gui\dialogs\EditGradientDialog.java:163: warning - Tag @author cannot be used in field documentation. It can only be used in the following types of documentation: overview, package, class/interface. src\edu\yale\csgp\vitapad\gui\dialogs\EnzymeDisplayPanel.java:50: warning - Tag @author cannot be used in field documentation. It can only be used in the following types of documentation: overview, package, class/interface. Building index for all the packages and classes... Building index for all classes... Generating target\docs\apidocs\help-doc.html... 171 warnings