+ try\r
+ {\r
+ Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();\r
+ Transferable contents = c.getContents(this);\r
+\r
+ if (contents == null)\r
+ {\r
+ return;\r
+ }\r
+\r
+ String str = (String) contents.getTransferData(DataFlavor.stringFlavor);\r
+ if(str.length()<1)\r
+ return;\r
+\r
+ String format = new IdentifyFile().Identify(str, "Paste");\r
+ SequenceI[] sequences;\r
+\r
+ if(Desktop.jalviewClipboard!=null)\r
+ {\r
+ // The clipboard was filled from within Jalview, we must use the sequences\r
+ // And dataset from the copied alignment\r
+ sequences = (SequenceI[])Desktop.jalviewClipboard[0];\r
+ }\r
+ else\r
+ {\r
+ sequences = new FormatAdapter().readFile(str, "Paste", format);\r
+ }\r
+\r
+ if (newAlignment)\r
+ {\r
+\r
+ Alignment alignment = new Alignment(sequences);\r
+\r
+ if(Desktop.jalviewClipboard!=null)\r
+ alignment.setDataset( (Alignment)Desktop.jalviewClipboard[1] );\r
+ else\r
+ alignment.setDataset( null );\r
+\r
+\r
+ AlignFrame af = new AlignFrame(alignment);\r
+ String newtitle = new String("Copied sequences");\r
+\r
+ //>>>This is a fix for the moment, until a better solution is found!!<<<\r
+ af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().transferSettings(\r
+ alignPanel.seqPanel.seqCanvas.getFeatureRenderer());\r
+\r
+\r
+ if (title.startsWith("Copied sequences"))\r
+ {\r
+ newtitle = title;\r
+ }\r
+ else\r
+ {\r
+ newtitle = newtitle.concat("- from " + title);\r
+ }\r
+\r
+ Desktop.addInternalFrame(af, newtitle, NEW_WINDOW_WIDTH,\r
+ NEW_WINDOW_HEIGHT);\r
+ }\r
+ else\r
+ {\r
+ //!newAlignment\r
+ for (int i = 0; i < sequences.length; i++)\r
+ {\r
+ Sequence newseq = new Sequence(sequences[i].getName(),\r
+ sequences[i].getSequence(), sequences[i].getStart(),\r
+ sequences[i].getEnd());\r
+ viewport.alignment.addSequence(newseq);\r
+ if(sequences[i].getDatasetSequence()==null)\r
+ {\r
+ ////////////////////////////\r
+ //Datset needs extension;\r
+ /////////////////////////////\r
+ Sequence ds = new Sequence(sequences[i].getName(),\r
+ AlignSeq.extractGaps("-. ", sequences[i].getSequence()),\r
+ sequences[i].getStart(),\r
+ sequences[i].getEnd());\r
+ newseq.setDatasetSequence(ds);\r
+ viewport.alignment.getDataset().addSequence(ds);\r
+ }\r
+ else\r
+ {\r
+ newseq.setDatasetSequence(sequences[i].getDatasetSequence());\r
+ if(sequences[i].getDatasetSequence().getAnnotation()!=null)\r
+ {\r
+ for(int aa=0; aa<sequences[i].getDatasetSequence().getAnnotation().length; aa++)\r
+ {\r
+ viewport.alignment.addAnnotation(sequences[i].getDatasetSequence().getAnnotation()[aa]);\r
+ }\r
+ }\r
+ }\r
+ }\r
+ viewport.setEndSeq(viewport.alignment.getHeight());\r
+ viewport.alignment.getWidth();\r
+ viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());\r
+ }\r
+ }\r
+ catch (Exception ex)\r
+ {\r
+ ex.printStackTrace();\r
+ System.out.println("Exception whilst pasting: "+ex);\r
+ // could be anything being pasted in here\r
+ }\r
+\r
+\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param e DOCUMENT ME!\r
+ */\r
+ protected void cut_actionPerformed(ActionEvent e)\r
+ {\r
+ copy_actionPerformed(null);\r
+ delete_actionPerformed(null);\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param e DOCUMENT ME!\r
+ */\r
+ protected void delete_actionPerformed(ActionEvent e)\r
+ {\r
+\r
+ if (viewport.getSelectionGroup() == null)\r
+ {\r
+ return;\r
+ }\r
+\r
+\r
+ SequenceGroup sg = viewport.getSelectionGroup();\r
+\r
+\r
+\r
+ //Jalview no longer allows deletion of residues.\r
+ //Check here whether any residues are in selection area\r
+ /* if( sg.getEndRes()-sg.getStartRes() < viewport.alignment.getWidth()-1)\r
+ {\r
+ for (int i = 0; i < sg.sequences.size(); i++)\r
+ {\r
+ SequenceI seq = sg.getSequenceAt(i);\r
+ int j = sg.getStartRes();\r
+ do\r
+ {\r
+ if (!jalview.util.Comparison.isGap(seq.getCharAt(j)))\r
+ {\r
+ JOptionPane.showInternalMessageDialog(\r
+ Desktop.desktop, "Cannot delete residues from alignment!\n"\r
+ + "Try hiding columns instead.",\r
+ "Deletion of residues not permitted",\r
+ JOptionPane.WARNING_MESSAGE);\r
+\r
+ return;\r
+ }\r
+ j++;\r
+ }while(j<=sg.getEndRes());\r
+ }\r
+ }*/\r
+\r
+\r
+ addHistoryItem(new HistoryItem("Delete Sequences", viewport.alignment,\r
+ HistoryItem.HIDE));\r
+\r
+\r
+ for (int i = 0; i < sg.sequences.size(); i++)\r
+ {\r
+ SequenceI seq = sg.getSequenceAt(i);\r
+ int index = viewport.getAlignment().findIndex(seq);\r
+\r
+ seq.deleteChars(sg.getStartRes(), sg.getEndRes() + 1);\r
+\r
+ // If the cut affects all sequences, remove highlighted columns\r
+ if (sg.sequences.size() == viewport.alignment.getHeight())\r
+ {\r
+ viewport.getColumnSelection().removeElements(sg.getStartRes(),\r
+ sg.getEndRes() + 1);\r
+ }\r
+\r
+ if (seq.getSequence().length() < 1)\r
+ {\r
+ viewport.getAlignment().deleteSequence(seq);\r
+ }\r
+ else\r
+ {\r
+ viewport.getAlignment().getSequences().setElementAt(seq, index);\r
+ }\r
+ }\r
+\r
+ viewport.setSelectionGroup(null);\r
+ viewport.alignment.deleteGroup(sg);\r
+\r
+ viewport.firePropertyChange("alignment", null,\r
+ viewport.getAlignment().getSequences());\r
+\r
+\r
+\r
+ if (viewport.getAlignment().getHeight() < 1)\r
+ {\r
+ try\r
+ {\r
+ this.setClosed(true);\r
+ }\r
+ catch (Exception ex)\r
+ {\r
+ }\r
+ }\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param e DOCUMENT ME!\r
+ */\r
+ protected void deleteGroups_actionPerformed(ActionEvent e)\r
+ {\r
+ viewport.alignment.deleteAllGroups();\r
+ viewport.setSelectionGroup(null);\r
+ alignPanel.repaint();\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param e DOCUMENT ME!\r
+ */\r
+ public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)\r
+ {\r
+ SequenceGroup sg = new SequenceGroup();\r
+\r
+ for (int i = 0; i < viewport.getAlignment().getSequences().size();\r
+ i++)\r
+ {\r
+ sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);\r
+ }\r
+\r
+ sg.setEndRes(viewport.alignment.getWidth() - 1);\r
+ viewport.setSelectionGroup(sg);\r
+ PaintRefresher.Refresh(null, viewport.alignment);\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param e DOCUMENT ME!\r
+ */\r
+ public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)\r
+ {\r
+ if(viewport.cursorMode)\r
+ {\r
+ alignPanel.seqPanel.keyboardNo1 = null;\r
+ alignPanel.seqPanel.keyboardNo2 = null;\r
+ }\r
+ viewport.setSelectionGroup(null);\r
+ viewport.getColumnSelection().clear();\r
+ viewport.setSelectionGroup(null);\r
+ alignPanel.seqPanel.seqCanvas.highlightSearchResults(null);\r
+ alignPanel.idPanel.idCanvas.searchResults = null;\r
+ PaintRefresher.Refresh(null, viewport.alignment);\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param e DOCUMENT ME!\r
+ */\r
+ public void invertSequenceMenuItem_actionPerformed(ActionEvent e)\r
+ {\r
+ SequenceGroup sg = viewport.getSelectionGroup();\r
+\r
+ if (sg == null)\r
+ {\r
+ selectAllSequenceMenuItem_actionPerformed(null);\r
+\r
+ return;\r
+ }\r
+\r
+ for (int i = 0; i < viewport.getAlignment().getSequences().size();\r
+ i++)\r
+ {\r
+ sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);\r
+ }\r
+\r
+ PaintRefresher.Refresh(null, viewport.alignment);\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param e DOCUMENT ME!\r
+ */\r
+ public void remove2LeftMenuItem_actionPerformed(ActionEvent e)\r
+ {\r
+ ColumnSelection colSel = viewport.getColumnSelection();\r
+\r
+ if (colSel.size() > 0)\r
+ {\r
+ addHistoryItem(new HistoryItem("Remove Left", viewport.alignment,\r
+ HistoryItem.HIDE));\r
+\r
+ int min = colSel.getMin();\r
+ viewport.getAlignment().trimLeft(min);\r
+ colSel.compensateForEdit(0, min);\r
+\r
+ if (viewport.getSelectionGroup() != null)\r
+ {\r
+ viewport.getSelectionGroup().adjustForRemoveLeft(min);\r
+ }\r
+\r
+ Vector groups = viewport.alignment.getGroups();\r
+\r
+ for (int i = 0; i < groups.size(); i++)\r
+ {\r
+ SequenceGroup sg = (SequenceGroup) groups.get(i);\r
+\r
+ if (!sg.adjustForRemoveLeft(min))\r
+ {\r
+ viewport.alignment.deleteGroup(sg);\r
+ }\r
+ }\r
+\r
+ viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());\r
+ }\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param e DOCUMENT ME!\r
+ */\r
+ public void remove2RightMenuItem_actionPerformed(ActionEvent e)\r
+ {\r
+ ColumnSelection colSel = viewport.getColumnSelection();\r
+\r
+ if (colSel.size() > 0)\r
+ {\r
+ addHistoryItem(new HistoryItem("Remove Right", viewport.alignment,\r
+ HistoryItem.HIDE));\r
+\r
+ int max = colSel.getMax();\r
+ viewport.getAlignment().trimRight(max);\r
+\r
+ if (viewport.getSelectionGroup() != null)\r
+ {\r
+ viewport.getSelectionGroup().adjustForRemoveRight(max);\r
+ }\r
+\r
+ Vector groups = viewport.alignment.getGroups();\r
+\r
+ for (int i = 0; i < groups.size(); i++)\r
+ {\r
+ SequenceGroup sg = (SequenceGroup) groups.get(i);\r
+\r
+ if (!sg.adjustForRemoveRight(max))\r
+ {\r
+ viewport.alignment.deleteGroup(sg);\r
+ }\r
+ }\r
+\r
+ viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());\r
+ }\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param e DOCUMENT ME!\r
+ */\r
+ public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)\r
+ {\r
+ addHistoryItem(new HistoryItem("Remove Gapped Columns",\r
+ viewport.alignment, HistoryItem.HIDE));\r
+\r
+ //This is to maintain viewport position on first residue\r
+ //of first sequence\r
+ SequenceI seq = viewport.alignment.getSequenceAt(0);\r
+ int startRes = seq.findPosition(viewport.startRes);\r
+\r
+ viewport.getAlignment().removeGaps();\r
+\r
+ viewport.setStartRes(seq.findIndex(startRes)-1);\r
+\r
+ viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param e DOCUMENT ME!\r
+ */\r
+ public void removeAllGapsMenuItem_actionPerformed(ActionEvent e)\r
+ {\r
+ addHistoryItem(new HistoryItem("Remove Gaps", viewport.alignment,\r
+ HistoryItem.HIDE));\r
+\r
+ //This is to maintain viewport position on first residue\r
+ //of first sequence\r
+ SequenceI seq = viewport.alignment.getSequenceAt(0);\r
+ int startRes = seq.findPosition(viewport.startRes);\r
+\r
+\r
+ SequenceI current;\r
+ int jSize;\r
+\r
+ Vector seqs = null;\r
+\r
+ int start = 0;\r
+ int end = viewport.alignment.getWidth();\r
+\r
+ if (viewport.getSelectionGroup() != null\r
+ && viewport.getSelectionGroup().sequences != null\r
+ && viewport.getSelectionGroup().sequences.size() > 0)\r
+ {\r
+ seqs = viewport.getSelectionGroup().sequences;\r
+ start = viewport.getSelectionGroup().getStartRes();\r
+ end = viewport.getSelectionGroup().getEndRes()+1;\r
+ }\r
+ else\r
+ {\r
+ seqs = viewport.alignment.getSequences();\r
+ }\r
+\r
+ for (int i = 0; i < seqs.size(); i++)\r
+ {\r
+ current = (SequenceI) seqs.elementAt(i);\r
+ jSize = current.getLength();\r
+\r
+ // Removing a range is much quicker than removing gaps\r
+ // one by one for long sequences\r
+ int j = start;\r
+ int rangeStart=-1, rangeEnd=-1;\r
+\r
+ do\r
+ {\r
+ if (jalview.util.Comparison.isGap(current.getCharAt(j)))\r
+ {\r
+ if(rangeStart==-1)\r
+ {\r
+ rangeStart = j;\r
+ rangeEnd = j+1;\r
+ }\r
+ else\r
+ {\r
+ rangeEnd++;\r
+ }\r
+ j++;\r
+ }\r
+ else\r
+ {\r
+ if(rangeStart>-1)\r
+ {\r
+ current.deleteChars(rangeStart, rangeEnd);\r
+ j-=rangeEnd-rangeStart;\r
+ jSize-=rangeEnd-rangeStart;\r
+ rangeStart = -1;\r
+ rangeEnd = -1;\r
+ }\r
+ else\r
+ j++;\r
+ }\r
+ }\r
+ while (j < end && j < jSize);\r
+ if(rangeStart>-1)\r
+ {\r
+ current.deleteChars(rangeStart, rangeEnd);\r
+ }\r
+ }\r
+\r
+ viewport.setStartRes(seq.findIndex(startRes)-1);\r
+\r
+ viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());\r
+ }\r
+\r
+ public void alignmentChanged()\r
+ {\r
+ if(viewport.padGaps)\r
+ viewport.getAlignment().padGaps();\r
+\r
+ if(viewport.vconsensus!=null && viewport.autoCalculateConsensus)\r
+ {\r
+ viewport.updateConsensus();\r
+ viewport.updateConservation();\r
+ }\r
+ resetAllColourSchemes();\r
+ if(alignPanel.overviewPanel!=null)\r
+ alignPanel.overviewPanel.updateOverviewImage();\r
+\r
+ viewport.alignment.adjustSequenceAnnotations();\r
+\r
+ alignPanel.repaint();\r
+ }\r
+\r
+ void resetAllColourSchemes()\r
+ {\r
+ ColourSchemeI cs = viewport.globalColourScheme;\r
+ if(cs!=null)\r
+ {\r
+ if (cs instanceof ClustalxColourScheme)\r
+ {\r
+ ( (ClustalxColourScheme) viewport.getGlobalColourScheme()).\r
+ resetClustalX(viewport.alignment.getSequences(),\r
+ viewport.alignment.getWidth());\r
+ }\r
+\r
+ cs.setConsensus(viewport.vconsensus);\r
+ if (cs.conservationApplied())\r
+ {\r
+ Alignment al = (Alignment) viewport.alignment;\r
+ Conservation c = new Conservation("All",\r
+ ResidueProperties.propHash, 3,\r
+ al.getSequences(), 0,\r
+ al.getWidth() - 1);\r
+ c.calculate();\r
+ c.verdict(false, viewport.ConsPercGaps);\r
+\r
+ cs.setConservation(c);\r
+ }\r
+ }\r
+\r
+ int s, sSize = viewport.alignment.getGroups().size();\r
+ for(s=0; s<sSize; s++)\r
+ {\r
+ SequenceGroup sg = (SequenceGroup)viewport.alignment.getGroups().elementAt(s);\r
+ if(sg.cs!=null && sg.cs instanceof ClustalxColourScheme)\r
+ {\r
+ ((ClustalxColourScheme)sg.cs).resetClustalX(sg.sequences, sg.getWidth());\r
+ }\r
+ sg.recalcConservation();\r
+ }\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param e DOCUMENT ME!\r
+ */\r
+ public void padGapsMenuitem_actionPerformed(ActionEvent e)\r
+ {\r
+ addHistoryItem(new HistoryItem("Pad Gaps", viewport.alignment,\r
+ HistoryItem.HIDE));\r
+\r
+ viewport.padGaps = padGapsMenuitem.isSelected();\r
+\r
+ // if (viewport.padGaps)\r
+ alignmentChanged();\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param e DOCUMENT ME!\r
+ */\r
+ public void findMenuItem_actionPerformed(ActionEvent e)\r
+ {\r
+ JInternalFrame frame = new JInternalFrame();\r
+ Finder finder = new Finder(viewport, alignPanel, frame);\r
+ frame.setContentPane(finder);\r
+ frame.setLayer(JLayeredPane.PALETTE_LAYER);\r
+ Desktop.addInternalFrame(frame, "Find", 340, 110);\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param e DOCUMENT ME!\r
+ */\r
+ public void font_actionPerformed(ActionEvent e)\r
+ {\r
+ new FontChooser(alignPanel);\r
+ }\r
+\r
+ public void smoothFont_actionPerformed(ActionEvent e)\r
+ {\r
+ viewport.antiAlias = smoothFont.isSelected();\r
+ alignPanel.annotationPanel.image = null;\r
+ alignPanel.repaint();\r
+ }\r
+\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param e DOCUMENT ME!\r
+ */\r
+ protected void seqLimit_actionPerformed(ActionEvent e)\r
+ {\r
+ viewport.setShowJVSuffix(seqLimits.isSelected());\r
+\r
+ alignPanel.idPanel.idCanvas.setPreferredSize(alignPanel.calculateIdWidth());\r
+ alignPanel.repaint();\r
+ }\r
+\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param e DOCUMENT ME!\r
+ */\r
+ protected void colourTextMenuItem_actionPerformed(ActionEvent e)\r
+ {\r
+ viewport.setColourText(colourTextMenuItem.isSelected());\r
+ alignPanel.repaint();\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param e DOCUMENT ME!\r
+ */\r
+ protected void wrapMenuItem_actionPerformed(ActionEvent e)\r
+ {\r
+ viewport.setWrapAlignment(wrapMenuItem.isSelected());\r
+ alignPanel.setWrapAlignment(wrapMenuItem.isSelected());\r
+ scaleAbove.setVisible(wrapMenuItem.isSelected());\r
+ scaleLeft.setVisible(wrapMenuItem.isSelected());\r
+ scaleRight.setVisible(wrapMenuItem.isSelected());\r
+ alignPanel.repaint();\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param e DOCUMENT ME!\r
+ */\r
+ protected void scaleAbove_actionPerformed(ActionEvent e)\r
+ {\r
+ viewport.setScaleAboveWrapped(scaleAbove.isSelected());\r
+ alignPanel.repaint();\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param e DOCUMENT ME!\r
+ */\r
+ protected void scaleLeft_actionPerformed(ActionEvent e)\r
+ {\r
+ viewport.setScaleLeftWrapped(scaleLeft.isSelected());\r
+ alignPanel.repaint();\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param e DOCUMENT ME!\r
+ */\r
+ protected void scaleRight_actionPerformed(ActionEvent e)\r
+ {\r
+ viewport.setScaleRightWrapped(scaleRight.isSelected());\r
+ alignPanel.repaint();\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param e DOCUMENT ME!\r
+ */\r
+ public void viewBoxesMenuItem_actionPerformed(ActionEvent e)\r
+ {\r
+ viewport.setShowBoxes(viewBoxesMenuItem.isSelected());\r
+ alignPanel.repaint();\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param e DOCUMENT ME!\r
+ */\r
+ public void viewTextMenuItem_actionPerformed(ActionEvent e)\r
+ {\r
+ viewport.setShowText(viewTextMenuItem.isSelected());\r
+ alignPanel.repaint();\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param e DOCUMENT ME!\r
+ */\r
+ protected void renderGapsMenuItem_actionPerformed(ActionEvent e)\r
+ {\r
+ viewport.setRenderGaps(renderGapsMenuItem.isSelected());\r
+ alignPanel.repaint();\r
+ }\r
+\r
+ public void fetchSeqFeatures_actionPerformed(ActionEvent e)\r
+ {\r
+ if (!viewport.alignment.isNucleotide())\r
+ {\r
+ new SequenceFeatureFetcher(viewport.\r
+ alignment,\r
+ alignPanel);\r
+ viewport.setShowSequenceFeatures(true);\r
+ showSeqFeatures.setSelected(true);\r
+ }\r
+ }\r
+\r
+\r
+ public void featureSettings_actionPerformed(ActionEvent e)\r
+ {\r
+ new FeatureSettings(viewport, alignPanel);\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param evt DOCUMENT ME!\r
+ */\r
+ public void showSeqFeatures_actionPerformed(ActionEvent evt)\r
+ {\r
+ viewport.setShowSequenceFeatures(showSeqFeatures.isSelected());\r
+ alignPanel.repaint();\r
+ if (alignPanel.getOverviewPanel() != null)\r
+ {\r
+ alignPanel.getOverviewPanel().updateOverviewImage();\r
+ }\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param e DOCUMENT ME!\r
+ */\r
+ public void annotationPanelMenuItem_actionPerformed(ActionEvent e)\r
+ {\r
+ viewport.setShowAnnotation(annotationPanelMenuItem.isSelected());\r
+ alignPanel.setAnnotationVisible(annotationPanelMenuItem.isSelected());\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param e DOCUMENT ME!\r
+ */\r
+ public void overviewMenuItem_actionPerformed(ActionEvent e)\r
+ {\r
+ if (alignPanel.overviewPanel != null)\r
+ {\r
+ return;\r
+ }\r
+\r
+ JInternalFrame frame = new JInternalFrame();\r
+ OverviewPanel overview = new OverviewPanel(alignPanel);\r
+ frame.setContentPane(overview);\r
+ Desktop.addInternalFrame(frame, "Overview " + this.getTitle(),\r
+ frame.getWidth(), frame.getHeight());\r
+ frame.pack();\r
+ frame.setLayer(JLayeredPane.PALETTE_LAYER);\r
+ frame.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()\r
+ {\r
+ public void internalFrameClosed(\r
+ javax.swing.event.InternalFrameEvent evt)\r
+ {\r
+ alignPanel.setOverviewPanel(null);\r
+ }\r
+ ;\r
+ });\r
+\r
+ alignPanel.setOverviewPanel(overview);\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param e DOCUMENT ME!\r
+ */\r
+ protected void noColourmenuItem_actionPerformed(ActionEvent e)\r
+ {\r
+ changeColour(null);\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param e DOCUMENT ME!\r
+ */\r
+ public void clustalColour_actionPerformed(ActionEvent e)\r
+ {\r
+ changeColour(new ClustalxColourScheme(\r
+ viewport.alignment.getSequences(), viewport.alignment.getWidth()));\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param e DOCUMENT ME!\r
+ */\r
+ public void zappoColour_actionPerformed(ActionEvent e)\r
+ {\r
+ changeColour(new ZappoColourScheme());\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param e DOCUMENT ME!\r
+ */\r
+ public void taylorColour_actionPerformed(ActionEvent e)\r
+ {\r
+ changeColour(new TaylorColourScheme());\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param e DOCUMENT ME!\r
+ */\r
+ public void hydrophobicityColour_actionPerformed(ActionEvent e)\r
+ {\r
+ changeColour(new HydrophobicColourScheme());\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param e DOCUMENT ME!\r
+ */\r
+ public void helixColour_actionPerformed(ActionEvent e)\r
+ {\r
+ changeColour(new HelixColourScheme());\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param e DOCUMENT ME!\r
+ */\r
+ public void strandColour_actionPerformed(ActionEvent e)\r
+ {\r
+ changeColour(new StrandColourScheme());\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param e DOCUMENT ME!\r
+ */\r
+ public void turnColour_actionPerformed(ActionEvent e)\r
+ {\r
+ changeColour(new TurnColourScheme());\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param e DOCUMENT ME!\r
+ */\r
+ public void buriedColour_actionPerformed(ActionEvent e)\r
+ {\r
+ changeColour(new BuriedColourScheme());\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param e DOCUMENT ME!\r
+ */\r
+ public void nucleotideColour_actionPerformed(ActionEvent e)\r
+ {\r
+ changeColour(new NucleotideColourScheme());\r
+ }\r
+\r
+ public void annotationColour_actionPerformed(ActionEvent e)\r
+ {\r
+ new AnnotationColourChooser(viewport, alignPanel);\r
+ }\r
+\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param e DOCUMENT ME!\r
+ */\r
+ protected void applyToAllGroups_actionPerformed(ActionEvent e)\r
+ {\r
+ viewport.setColourAppliesToAllGroups(applyToAllGroups.isSelected());\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param cs DOCUMENT ME!\r
+ */\r
+ void changeColour(ColourSchemeI cs)\r
+ {\r
+ int threshold = 0;\r
+\r
+ if(cs!=null)\r
+ {\r
+ if (viewport.getAbovePIDThreshold())\r
+ {\r
+ threshold = SliderPanel.setPIDSliderSource(alignPanel, cs,\r
+ "Background");\r
+\r
+ cs.setThreshold(threshold,\r
+ viewport.getIgnoreGapsConsensus());\r
+\r
+ viewport.setGlobalColourScheme(cs);\r
+ }\r
+ else\r
+ {\r
+ cs.setThreshold(0, viewport.getIgnoreGapsConsensus());\r
+ }\r
+\r
+ if (viewport.getConservationSelected())\r
+ {\r
+\r
+ Alignment al = (Alignment) viewport.alignment;\r
+ Conservation c = new Conservation("All",\r
+ ResidueProperties.propHash, 3,\r
+ al.getSequences(), 0,\r
+ al.getWidth() - 1);\r
+\r
+ c.calculate();\r
+ c.verdict(false, viewport.ConsPercGaps);\r
+\r
+ cs.setConservation(c);\r
+\r
+ cs.setConservationInc(SliderPanel.setConservationSlider(alignPanel, cs,\r
+ "Background"));\r
+ }\r
+ else\r
+ {\r
+ cs.setConservation(null);\r
+ }\r
+\r
+ cs.setConsensus(viewport.vconsensus);\r
+ }\r
+\r
+ viewport.setGlobalColourScheme(cs);\r
+\r
+ if (viewport.getColourAppliesToAllGroups())\r
+ {\r
+ Vector groups = viewport.alignment.getGroups();\r
+\r
+ for (int i = 0; i < groups.size(); i++)\r
+ {\r
+ SequenceGroup sg = (SequenceGroup) groups.elementAt(i);\r
+\r
+ if (cs == null)\r
+ {\r
+ sg.cs = null;\r
+ continue;\r
+ }\r
+\r
+ if (cs instanceof ClustalxColourScheme)\r
+ {\r
+ sg.cs = new ClustalxColourScheme(sg.sequences, sg.getWidth());\r
+ }\r
+ else if (cs instanceof UserColourScheme)\r
+ {\r
+ sg.cs = new UserColourScheme( ( (UserColourScheme) cs).getColours());\r
+ }\r
+ else\r
+ {\r
+ try\r
+ {\r
+ sg.cs = (ColourSchemeI) cs.getClass().newInstance();\r
+ }\r
+ catch (Exception ex)\r
+ {\r
+ }\r
+ }\r
+\r
+ if (viewport.getAbovePIDThreshold()\r
+ || cs instanceof PIDColourScheme\r
+ || cs instanceof Blosum62ColourScheme)\r
+ {\r
+ sg.cs.setThreshold(threshold,\r
+ viewport.getIgnoreGapsConsensus());\r
+\r
+ sg.cs.setConsensus(AAFrequency.calculate(sg.sequences, 0,\r
+ sg.getWidth()));\r
+ }\r
+ else\r
+ sg.cs.setThreshold(0, viewport.getIgnoreGapsConsensus());\r
+\r
+\r
+ if (viewport.getConservationSelected())\r
+ {\r
+ Conservation c = new Conservation("Group",\r
+ ResidueProperties.propHash, 3,\r
+ sg.sequences, 0,\r
+ viewport.alignment.getWidth() - 1);\r
+ c.calculate();\r
+ c.verdict(false, viewport.ConsPercGaps);\r
+ sg.cs.setConservation(c);\r
+ }\r
+ else\r
+ sg.cs.setConservation(null);\r
+ }\r
+ }\r
+\r
+ if (alignPanel.getOverviewPanel() != null)\r
+ {\r
+ alignPanel.getOverviewPanel().updateOverviewImage();\r
+ }\r
+\r
+ alignPanel.repaint();\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param e DOCUMENT ME!\r
+ */\r
+ protected void modifyPID_actionPerformed(ActionEvent e)\r
+ {\r
+ if (viewport.getAbovePIDThreshold() && viewport.globalColourScheme!=null)\r
+ {\r
+ SliderPanel.setPIDSliderSource(alignPanel,\r
+ viewport.getGlobalColourScheme(),\r
+ "Background");\r
+ SliderPanel.showPIDSlider();\r
+ }\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param e DOCUMENT ME!\r
+ */\r
+ protected void modifyConservation_actionPerformed(ActionEvent e)\r
+ {\r
+ if (viewport.getConservationSelected() && viewport.globalColourScheme!=null)\r
+ {\r
+ SliderPanel.setConservationSlider(alignPanel,\r
+ viewport.globalColourScheme,\r
+ "Background");\r
+ SliderPanel.showConservationSlider();\r
+ }\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param e DOCUMENT ME!\r
+ */\r
+ protected void conservationMenuItem_actionPerformed(ActionEvent e)\r
+ {\r
+ viewport.setConservationSelected(conservationMenuItem.isSelected());\r
+\r
+ viewport.setAbovePIDThreshold(false);\r
+ abovePIDThreshold.setSelected(false);\r
+\r
+ changeColour(viewport.getGlobalColourScheme());\r
+\r
+ modifyConservation_actionPerformed(null);\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param e DOCUMENT ME!\r
+ */\r
+ public void abovePIDThreshold_actionPerformed(ActionEvent e)\r
+ {\r
+ viewport.setAbovePIDThreshold(abovePIDThreshold.isSelected());\r
+\r
+ conservationMenuItem.setSelected(false);\r
+ viewport.setConservationSelected(false);\r
+\r
+ changeColour(viewport.getGlobalColourScheme());\r
+\r
+ modifyPID_actionPerformed(null);\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param e DOCUMENT ME!\r
+ */\r
+ public void userDefinedColour_actionPerformed(ActionEvent e)\r
+ {\r
+ if (e.getActionCommand().equals("User Defined..."))\r
+ {\r
+ new UserDefinedColours(alignPanel, null);\r
+ }\r
+ else\r
+ {\r
+ UserColourScheme udc = (UserColourScheme) UserDefinedColours.\r
+ getUserColourSchemes().get(e.getActionCommand());\r
+\r
+ changeColour(udc);\r
+ }\r
+ }\r
+\r
+ public void updateUserColourMenu()\r
+ {\r
+\r
+ Component[] menuItems = colourMenu.getMenuComponents();\r
+ int i, iSize = menuItems.length;\r
+ for (i = 0; i < iSize; i++)\r
+ {\r
+ if (menuItems[i].getName() != null &&\r
+ menuItems[i].getName().equals("USER_DEFINED"))\r
+ {\r
+ colourMenu.remove(menuItems[i]);\r
+ iSize--;\r
+ }\r
+ }\r
+ if (jalview.gui.UserDefinedColours.getUserColourSchemes() != null)\r
+ {\r
+ java.util.Enumeration userColours = jalview.gui.UserDefinedColours.\r
+ getUserColourSchemes().keys();\r
+\r
+ while (userColours.hasMoreElements())\r
+ {\r
+ final JRadioButtonMenuItem radioItem = new JRadioButtonMenuItem(userColours.\r
+ nextElement().toString());\r
+ radioItem.setName("USER_DEFINED");\r
+ radioItem.addMouseListener(new MouseAdapter()\r
+ {\r
+ public void mousePressed(MouseEvent evt)\r
+ {\r
+ if(evt.isControlDown() || SwingUtilities.isRightMouseButton(evt))\r
+ {\r
+ radioItem.removeActionListener(radioItem.getActionListeners()[0]);\r
+\r
+ int option = JOptionPane.showInternalConfirmDialog(jalview.gui.Desktop.desktop,\r
+ "Remove from default list?",\r
+ "Remove user defined colour",\r
+ JOptionPane.YES_NO_OPTION);\r
+ if(option == JOptionPane.YES_OPTION)\r
+ {\r
+ jalview.gui.UserDefinedColours.removeColourFromDefaults(radioItem.getText());\r
+ colourMenu.remove(radioItem);\r
+ }\r
+ else\r
+ radioItem.addActionListener(new ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent evt)\r
+ {\r
+ userDefinedColour_actionPerformed(evt);\r
+ }\r
+ });\r
+ }\r
+ }\r
+ });\r
+ radioItem.addActionListener(new ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent evt)\r
+ {\r
+ userDefinedColour_actionPerformed(evt);\r
+ }\r
+ });\r
+\r
+ colourMenu.insert(radioItem, 15);\r
+ colours.add(radioItem);\r
+ }\r
+ }\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param e DOCUMENT ME!\r
+ */\r
+ public void PIDColour_actionPerformed(ActionEvent e)\r
+ {\r
+ changeColour(new PIDColourScheme());\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param e DOCUMENT ME!\r
+ */\r
+ public void BLOSUM62Colour_actionPerformed(ActionEvent e)\r
+ {\r
+ changeColour(new Blosum62ColourScheme());\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param e DOCUMENT ME!\r
+ */\r
+ public void sortPairwiseMenuItem_actionPerformed(ActionEvent e)\r
+ {\r
+ addHistoryItem(new HistoryItem("Pairwise Sort", viewport.alignment,\r
+ HistoryItem.SORT));\r
+ AlignmentSorter.sortByPID(viewport.getAlignment(),\r
+ viewport.getAlignment().getSequenceAt(0));\r
+ alignPanel.repaint();\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param e DOCUMENT ME!\r
+ */\r
+ public void sortIDMenuItem_actionPerformed(ActionEvent e)\r
+ {\r
+ addHistoryItem(new HistoryItem("ID Sort", viewport.alignment,\r
+ HistoryItem.SORT));\r
+ AlignmentSorter.sortByID(viewport.getAlignment());\r
+ alignPanel.repaint();\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param e DOCUMENT ME!\r
+ */\r
+ public void sortGroupMenuItem_actionPerformed(ActionEvent e)\r
+ {\r
+ addHistoryItem(new HistoryItem("Group Sort", viewport.alignment,\r
+ HistoryItem.SORT));\r
+\r
+ AlignmentSorter.sortByGroup(viewport.getAlignment());\r
+ alignPanel.repaint();\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param e DOCUMENT ME!\r
+ */\r
+ public void removeRedundancyMenuItem_actionPerformed(ActionEvent e)\r
+ {\r
+ RedundancyPanel sp = new RedundancyPanel(alignPanel, this);\r
+ JInternalFrame frame = new JInternalFrame();\r
+ frame.setContentPane(sp);\r
+ Desktop.addInternalFrame(frame, "Redundancy threshold selection", 400,\r
+ 100, false);\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param e DOCUMENT ME!\r
+ */\r
+ public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)\r
+ {\r
+ if ( (viewport.getSelectionGroup() == null) ||\r
+ (viewport.getSelectionGroup().getSize() < 2))\r
+ {\r
+ JOptionPane.showInternalMessageDialog(this,\r
+ "You must select at least 2 sequences.",\r
+ "Invalid Selection",\r
+ JOptionPane.WARNING_MESSAGE);\r
+ }\r
+ else\r
+ {\r
+ JInternalFrame frame = new JInternalFrame();\r
+ frame.setContentPane(new PairwiseAlignPanel(viewport));\r
+ Desktop.addInternalFrame(frame, "Pairwise Alignment", 600, 500);\r
+ }\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param e DOCUMENT ME!\r
+ */\r
+ public void PCAMenuItem_actionPerformed(ActionEvent e)\r
+ {\r
+ if ( ( (viewport.getSelectionGroup() != null) &&\r
+ (viewport.getSelectionGroup().getSize() < 4) &&\r
+ (viewport.getSelectionGroup().getSize() > 0)) ||\r
+ (viewport.getAlignment().getHeight() < 4))\r
+ {\r
+ JOptionPane.showInternalMessageDialog(this,\r
+ "Principal component analysis must take\n" +\r
+ "at least 4 input sequences.",\r
+ "Sequence selection insufficient",\r
+ JOptionPane.WARNING_MESSAGE);\r
+\r
+ return;\r
+ }\r
+\r
+ new PCAPanel(viewport);\r
+ }\r
+\r
+\r
+ public void autoCalculate_actionPerformed(ActionEvent e)\r
+ {\r
+ viewport.autoCalculateConsensus = autoCalculate.isSelected();\r
+ }\r
+\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param e DOCUMENT ME!\r
+ */\r
+ public void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)\r
+ {\r
+ NewTreePanel("AV", "PID", "Average distance tree using PID");\r