-/********************\r
- * 2004 Jalview Reengineered\r
- * Barton Group\r
- * Dundee University\r
+/*\r
+ * Jalview - A Sequence Alignment Editor and Viewer\r
+ * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
*\r
- * AM Waterhouse\r
- *******************/\r
-\r
-\r
-\r
+ * This program is free software; you can redistribute it and/or\r
+ * modify it under the terms of the GNU General Public License\r
+ * as published by the Free Software Foundation; either version 2\r
+ * of the License, or (at your option) any later version.\r
+ *\r
+ * This program is distributed in the hope that it will be useful,\r
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of\r
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\r
+ * GNU General Public License for more details.\r
+ *\r
+ * You should have received a copy of the GNU General Public License\r
+ * along with this program; if not, write to the Free Software\r
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
+ */\r
\r
package jalview.appletgui;\r
\r
-import jalview.jbappletgui.GAlignFrame;\r
import jalview.schemes.*;\r
import jalview.datamodel.*;\r
import jalview.analysis.*;\r
import jalview.io.*;\r
+import jalview.commands.*;\r
import java.awt.*;\r
import java.awt.event.*;\r
import java.util.*;\r
+import java.io.InputStreamReader;\r
+import java.io.BufferedReader;\r
+import java.net.URL;\r
\r
\r
-public class AlignFrame extends GAlignFrame\r
+public class AlignFrame extends Frame implements ActionListener,\r
+ ItemListener, KeyListener, MouseListener\r
{\r
- final AlignmentPanel alignPanel;\r
- final AlignViewport viewport;\r
- public static final int NEW_WINDOW_WIDTH = 700;\r
- public static final int NEW_WINDOW_HEIGHT = 500;\r
- jalview.bin.JalviewLite applet;\r
+ public AlignmentPanel alignPanel;\r
+ public AlignViewport viewport;\r
+ int DEFAULT_WIDTH = 700;\r
+ int DEFAULT_HEIGHT = 500;\r
+\r
+ String jalviewServletURL;\r
\r
- public AlignFrame(AlignmentI al)\r
- {\r
- this.applet = null;\r
- viewport = new AlignViewport(al, null);\r
- alignPanel = new AlignmentPanel(this, viewport);\r
- add(alignPanel);\r
- alignPanel.validate();\r
- }\r
\r
- public AlignFrame(AlignmentI al, jalview.bin.JalviewLite applet)\r
+ public AlignFrame(AlignmentI al,\r
+ jalview.bin.JalviewLite applet,\r
+ String title,\r
+ boolean embedded)\r
{\r
- this.applet = applet;\r
+\r
+ jalviewServletURL = applet.getParameter("APPLICATION_URL");\r
+\r
+ try{\r
+ jbInit();\r
+ }catch(Exception ex)\r
+ {\r
+ ex.printStackTrace();\r
+ }\r
+\r
viewport = new AlignViewport(al, applet);\r
alignPanel = new AlignmentPanel(this, viewport);\r
- add(alignPanel);\r
- alignPanel.validate();\r
\r
- String treeFile = applet.getParameter("treeFile");\r
- TreePanel treepanel = null;\r
- if (treeFile != null)\r
+ viewport.updateConservation(alignPanel);\r
+ viewport.updateConsensus(alignPanel);\r
+\r
+ annotationPanelMenuItem.setState(viewport.showAnnotation);\r
+\r
+ seqLimits.setState(viewport.showJVSuffix);\r
+\r
+ if(applet!=null)\r
{\r
- try\r
+ String param = applet.getParameter("sortBy");\r
+ if (param != null)\r
{\r
- treeFile = treeFile;\r
- jalview.io.NewickFile fin = new jalview.io.NewickFile( applet.getCodeBase()+treeFile, "URL");\r
- fin.parse();\r
+ if (param.equalsIgnoreCase("Id"))\r
+ sortIDMenuItem_actionPerformed();\r
+ else if (param.equalsIgnoreCase("Pairwise Identity"))\r
+ sortPairwiseMenuItem_actionPerformed();\r
+ }\r
\r
- if (fin.getTree() != null)\r
+ param = applet.getParameter("wrap");\r
+ if (param != null)\r
+ {\r
+ if (param.equalsIgnoreCase("true"))\r
{\r
- TreePanel tp = null;\r
- tp = new TreePanel(viewport, viewport.getAlignment().getSequences(),\r
- fin, "FromFile", applet.getCodeBase()+treeFile);\r
- jalview.bin.JalviewLite.addFrame(tp, treeFile, 600, 500);\r
- addTreeMenuItem(tp, treeFile);\r
+ wrapMenuItem.setState(true);\r
+ wrapMenuItem_actionPerformed();\r
}\r
}\r
- catch (Exception ex)\r
+\r
+ try\r
{\r
- ex.printStackTrace();\r
+ param = applet.getParameter("windowWidth");\r
+ if (param != null)\r
+ {\r
+ int width = Integer.parseInt(param);\r
+ DEFAULT_WIDTH = width;\r
+ }\r
+ param = applet.getParameter("windowHeight");\r
+ if (param != null)\r
+ {\r
+ int height = Integer.parseInt(param);\r
+ DEFAULT_HEIGHT = height;\r
+ }\r
}\r
+ catch (Exception ex)\r
+ {}\r
+\r
}\r
\r
+ //Some JVMS send keyevents to Top frame or lowest panel,\r
+ //Havent worked out why yet. So add to both this frame and seqCanvas for now\r
+ this.addKeyListener(this);\r
+ alignPanel.seqPanel.seqCanvas.addKeyListener(this);\r
+ alignPanel.idPanel.idCanvas.addKeyListener(this);\r
+ alignPanel.scalePanel.addKeyListener(this);\r
+ alignPanel.annotationPanel.addKeyListener(this);\r
+\r
+\r
+ if(embedded)\r
+ {\r
+ setEmbedded();\r
+ }\r
+ else\r
+ {\r
+ add(alignPanel, BorderLayout.CENTER);\r
+ jalview.bin.JalviewLite.addFrame(this, title, DEFAULT_WIDTH,\r
+ DEFAULT_HEIGHT);\r
+ }\r
+ alignPanel.validate();\r
+ alignPanel.repaint();\r
+ }\r
+ public AlignViewport getAlignViewport()\r
+ {\r
+ return viewport;\r
+ }\r
\r
+ public SeqCanvas getSeqcanvas()\r
+ {\r
+ return alignPanel.seqPanel.seqCanvas;\r
}\r
\r
- public void inputText_actionPerformed(ActionEvent e)\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param String DOCUMENT ME!\r
+ */\r
+\r
+ public void parseFeaturesFile(String file, String type)\r
{\r
- CutAndPasteTransfer cap = new CutAndPasteTransfer(true);\r
- Frame frame = new Frame();\r
- frame.add(cap);\r
- jalview.bin.JalviewLite.addFrame(frame, "Cut & Paste Input", 500,500);\r
+ Hashtable featureLinks = new Hashtable();\r
+ boolean featuresFile = false;\r
+ try{\r
+ featuresFile = new jalview.io.FeaturesFile(file, type).parse(viewport.alignment,\r
+ alignPanel.seqPanel.seqCanvas.\r
+ getFeatureRenderer().featureColours,\r
+ featureLinks,\r
+ true);\r
+ }\r
+ catch(Exception ex)\r
+ {\r
+ ex.printStackTrace();\r
+ }\r
+\r
+ if(featuresFile)\r
+ {\r
+ if(featureLinks.size()>0)\r
+ alignPanel.seqPanel.seqCanvas\r
+ .getFeatureRenderer().featureLinks = featureLinks;\r
+ viewport.showSequenceFeatures = true;\r
+ sequenceFeatures.setState(true);\r
+ alignPanel.repaint();\r
+ }\r
+\r
+ }\r
+\r
+\r
+ public void keyPressed(KeyEvent evt)\r
+ {\r
+ if (viewport.cursorMode\r
+ && evt.getKeyCode() >= KeyEvent.VK_0\r
+ && evt.getKeyCode() <= KeyEvent.VK_9)\r
+ {\r
+ alignPanel.seqPanel.numberPressed(evt.getKeyChar());\r
+ }\r
+\r
+ switch (evt.getKeyCode())\r
+ {\r
+ case 27: // escape key\r
+ deselectAllSequenceMenuItem_actionPerformed();\r
+ break;\r
+ case KeyEvent.VK_X:\r
+ if (evt.isControlDown() || evt.isMetaDown())\r
+ {\r
+ cut_actionPerformed();\r
+ }\r
+ break;\r
+ case KeyEvent.VK_C:\r
+ if (viewport.cursorMode && !evt.isControlDown())\r
+ {\r
+ alignPanel.seqPanel.setCursorColumn();\r
+ }\r
+ if (evt.isControlDown() || evt.isMetaDown())\r
+ {\r
+ copy_actionPerformed();\r
+ }\r
+ break;\r
+ case KeyEvent.VK_V:\r
+ if (evt.isControlDown())\r
+ {\r
+ paste(evt.isShiftDown());\r
+ }\r
+ break;\r
+ case KeyEvent.VK_A:\r
+ if (evt.isControlDown() || evt.isMetaDown())\r
+ {\r
+ selectAllSequenceMenuItem_actionPerformed();\r
+ }\r
+ break;\r
+ case KeyEvent.VK_DOWN:\r
+ if(viewport.cursorMode)\r
+ {\r
+ alignPanel.seqPanel.moveCursor(0,1);\r
+ }\r
+ else\r
+ moveSelectedSequences(false);\r
+ break;\r
+\r
+ case KeyEvent.VK_UP:\r
+ if (viewport.cursorMode)\r
+ {\r
+ alignPanel.seqPanel.moveCursor(0,-1);\r
+ }\r
+ else\r
+ moveSelectedSequences(true);\r
+ break;\r
+\r
+ case KeyEvent.VK_LEFT:\r
+ if(viewport.cursorMode)\r
+ {\r
+ alignPanel.seqPanel.moveCursor(-1,0);\r
+ }\r
+ break;\r
+\r
+ case KeyEvent.VK_RIGHT:\r
+ if (viewport.cursorMode)\r
+ {\r
+ alignPanel.seqPanel.moveCursor(1,0);\r
+ }\r
+ break;\r
+ case KeyEvent.VK_SPACE:\r
+ if(viewport.cursorMode)\r
+ {\r
+ alignPanel.seqPanel.insertGapAtCursor(evt.isControlDown()\r
+ || evt.isShiftDown()\r
+ || evt.isAltDown()\r
+ );\r
+ }\r
+ break;\r
+\r
+ case KeyEvent.VK_DELETE:\r
+ case KeyEvent.VK_BACK_SPACE:\r
+ if(viewport.cursorMode)\r
+ {\r
+ alignPanel.seqPanel.deleteGapAtCursor(evt.isControlDown()\r
+ || evt.isShiftDown()\r
+ || evt.isAltDown());\r
+ }\r
+ else\r
+ {\r
+ cut_actionPerformed();\r
+ alignPanel.seqPanel.seqCanvas.repaint();\r
+ }\r
+ break;\r
+\r
+ case KeyEvent.VK_S:\r
+ if(viewport.cursorMode)\r
+ {\r
+ alignPanel.seqPanel.setCursorRow();\r
+ }\r
+ break;\r
+ case KeyEvent.VK_P:\r
+ if(viewport.cursorMode)\r
+ {\r
+ alignPanel.seqPanel.setCursorPosition();\r
+ }\r
+ break;\r
+\r
+ case KeyEvent.VK_ENTER:\r
+ case KeyEvent.VK_COMMA:\r
+ if(viewport.cursorMode)\r
+ {\r
+ alignPanel.seqPanel.setCursorRowAndColumn();\r
+ }\r
+ break;\r
+\r
+ case KeyEvent.VK_Q:\r
+ if(viewport.cursorMode)\r
+ {\r
+ alignPanel.seqPanel.setSelectionAreaAtCursor(true);\r
+ }\r
+ break;\r
+ case KeyEvent.VK_M:\r
+ if(viewport.cursorMode)\r
+ {\r
+ alignPanel.seqPanel.setSelectionAreaAtCursor(false);\r
+ }\r
+ break;\r
+\r
+ case KeyEvent.VK_F2:\r
+ viewport.cursorMode = ! viewport.cursorMode;\r
+ statusBar.setText("Keyboard editing mode is "+\r
+ (viewport.cursorMode ? "on" : "off"));\r
+ if(viewport.cursorMode)\r
+ {\r
+ alignPanel.seqPanel.seqCanvas.cursorX = viewport.startRes;\r
+ alignPanel.seqPanel.seqCanvas.cursorY = viewport.startSeq;\r
+ }\r
+ break;\r
+\r
+ case KeyEvent.VK_F:\r
+ if (evt.isControlDown())\r
+ {\r
+ findMenuItem_actionPerformed();\r
+ }\r
+ break;\r
+\r
+ case KeyEvent.VK_H:\r
+ {\r
+ boolean toggleSeqs = !evt.isControlDown();\r
+ boolean toggleCols = !evt.isShiftDown();\r
+ boolean hide = false;\r
+ SequenceGroup sg = viewport.getSelectionGroup();\r
+\r
+ if(toggleSeqs)\r
+ {\r
+ if (sg != null && sg.getSize(false) != viewport.alignment.getHeight())\r
+ {\r
+ hide = true;\r
+ viewport.hideAllSelectedSeqs();\r
+ }\r
+ else if (!(toggleCols && viewport.colSel.getSelected().size() > 0))\r
+ viewport.showAllHiddenSeqs();\r
+ }\r
+\r
+ if(toggleCols)\r
+ {\r
+ if (viewport.colSel.getSelected().size() > 0)\r
+ {\r
+ viewport.hideSelectedColumns();\r
+ if(!toggleSeqs)\r
+ viewport.selectionGroup = sg;\r
+ }\r
+ else if (!hide)\r
+ viewport.showAllHiddenColumns();\r
+ }\r
+ break;\r
+ }\r
+\r
+ case KeyEvent.VK_PAGE_UP:\r
+ if (viewport.wrapAlignment)\r
+ alignPanel.scrollUp(true);\r
+ else\r
+ alignPanel.setScrollValues(viewport.startRes,\r
+ viewport.startSeq\r
+ - viewport.endSeq + viewport.startSeq);\r
+ break;\r
+\r
+ case KeyEvent.VK_PAGE_DOWN:\r
+ if (viewport.wrapAlignment)\r
+ alignPanel.scrollUp(false);\r
+ else\r
+ alignPanel.setScrollValues(viewport.startRes,\r
+ viewport.startSeq\r
+ + viewport.endSeq - viewport.startSeq);\r
+ break;\r
+\r
+ case KeyEvent.VK_Z:\r
+ if (evt.isControlDown())\r
+ {\r
+ undoMenuItem_actionPerformed();\r
+ }\r
+ break;\r
+\r
+ case KeyEvent.VK_Y:\r
+ if (evt.isControlDown())\r
+ {\r
+ redoMenuItem_actionPerformed();\r
+ }\r
+ break;\r
+\r
+ case KeyEvent.VK_L:\r
+ if (evt.isControlDown())\r
+ {\r
+ trimAlignment(true);\r
+ }\r
+ break;\r
+\r
+ case KeyEvent.VK_R:\r
+ if (evt.isControlDown())\r
+ {\r
+ trimAlignment(false);\r
+ }\r
+ break;\r
+\r
+ case KeyEvent.VK_E:\r
+ if (evt.isControlDown())\r
+ {\r
+ if (evt.isShiftDown())\r
+ this.removeAllGapsMenuItem_actionPerformed();\r
+ else\r
+ removeGappedColumnMenuItem_actionPerformed();\r
+ }\r
+ break;\r
+ case KeyEvent.VK_I:\r
+ if (evt.isControlDown())\r
+ {\r
+ if (evt.isAltDown())\r
+ viewport.invertColumnSelection();\r
+ else\r
+ this.invertSequenceMenuItem_actionPerformed();\r
+ }\r
+ break;\r
+\r
+ case KeyEvent.VK_U:\r
+ if (evt.isControlDown())\r
+ {\r
+ this.deleteGroups_actionPerformed();\r
+ }\r
+ break;\r
+\r
+ case KeyEvent.VK_T:\r
+ if (evt.isControlDown())\r
+ {\r
+ newView();\r
+ }\r
+ break;\r
+\r
+\r
+ }\r
+ alignPanel.repaint();\r
}\r
+ public void keyReleased(KeyEvent evt)\r
+ {}\r
+ public void keyTyped(KeyEvent evt)\r
+ {}\r
+\r
+public void itemStateChanged(ItemEvent evt)\r
+ {\r
+ if(evt.getSource()==colourTextMenuItem)\r
+ colourTextMenuItem_actionPerformed();\r
+ else if(evt.getSource()==wrapMenuItem)\r
+ wrapMenuItem_actionPerformed();\r
+ else if(evt.getSource()==scaleAbove)\r
+ viewport.setScaleAboveWrapped(scaleAbove.getState());\r
+ else if(evt.getSource()==scaleLeft)\r
+ viewport.setScaleLeftWrapped(scaleLeft.getState());\r
+ else if(evt.getSource()==scaleRight)\r
+ viewport.setScaleRightWrapped(scaleRight.getState());\r
+ else if(evt.getSource()==seqLimits)\r
+ seqLimits_itemStateChanged();\r
+ else if(evt.getSource()==viewBoxesMenuItem)\r
+ viewport.setShowBoxes(viewBoxesMenuItem.getState());\r
+ else if(evt.getSource()==viewTextMenuItem)\r
+ viewport.setShowText(viewTextMenuItem.getState());\r
+ else if(evt.getSource()==renderGapsMenuItem)\r
+ viewport.setRenderGaps(renderGapsMenuItem.getState());\r
+ else if(evt.getSource()==annotationPanelMenuItem)\r
+ {\r
+ viewport.setShowAnnotation(annotationPanelMenuItem.getState());\r
+ alignPanel.setAnnotationVisible(annotationPanelMenuItem.getState());\r
+ }\r
+ else if(evt.getSource()==sequenceFeatures)\r
+ {\r
+ viewport.showSequenceFeatures(sequenceFeatures.getState());\r
+ alignPanel.seqPanel.seqCanvas.repaint();\r
+ }\r
+ else if(evt.getSource()==conservationMenuItem)\r
+ conservationMenuItem_actionPerformed();\r
+ else if(evt.getSource()==abovePIDThreshold)\r
+ abovePIDThreshold_actionPerformed();\r
+ else if(evt.getSource()==applyToAllGroups)\r
+ viewport.setColourAppliesToAllGroups(applyToAllGroups.getState());\r
+ else if(evt.getSource()==autoCalculate)\r
+ viewport.autocalculateConsensus = autoCalculate.getState();\r
\r
+ alignPanel.repaint();\r
+ }\r
+ public void actionPerformed(ActionEvent evt)\r
+ {\r
+ Object source = evt.getSource();\r
+\r
+ if(source==inputText)\r
+ inputText_actionPerformed();\r
+ else if(source==loadTree)\r
+ loadTree_actionPerformed();\r
+ else if(source==loadApplication)\r
+ launchFullApplication();\r
+ else if(source==closeMenuItem)\r
+ closeMenuItem_actionPerformed();\r
+ else if(source==copy)\r
+ copy_actionPerformed();\r
+ else if(source==undoMenuItem)\r
+ undoMenuItem_actionPerformed();\r
+ else if(source==redoMenuItem)\r
+ redoMenuItem_actionPerformed();\r
+ else if(source==inputText)\r
+ inputText_actionPerformed();\r
+ else if(source==closeMenuItem)\r
+ closeMenuItem_actionPerformed();\r
+ else if(source==undoMenuItem)\r
+ undoMenuItem_actionPerformed();\r
+ else if(source==redoMenuItem)\r
+ redoMenuItem_actionPerformed();\r
+ else if(source==copy)\r
+ copy_actionPerformed();\r
+ else if(source==pasteNew)\r
+ pasteNew_actionPerformed();\r
+ else if(source==pasteThis)\r
+ pasteThis_actionPerformed();\r
+ else if(source==cut)\r
+ cut_actionPerformed();\r
+ else if(source==delete)\r
+ delete_actionPerformed();\r
+ else if(source==deleteGroups)\r
+ deleteGroups_actionPerformed();\r
+ else if(source==selectAllSequenceMenuItem)\r
+ selectAllSequenceMenuItem_actionPerformed();\r
+ else if(source==deselectAllSequenceMenuItem)\r
+ deselectAllSequenceMenuItem_actionPerformed();\r
+ else if(source==invertSequenceMenuItem)\r
+ invertSequenceMenuItem_actionPerformed();\r
+ else if(source==invertColSel)\r
+ { viewport.invertColumnSelection(); alignPanel.repaint(); }\r
+ else if(source==remove2LeftMenuItem)\r
+ trimAlignment(true);\r
+ else if(source==remove2RightMenuItem)\r
+ trimAlignment(false);\r
+ else if(source==removeGappedColumnMenuItem)\r
+ removeGappedColumnMenuItem_actionPerformed();\r
+ else if(source==removeAllGapsMenuItem)\r
+ removeAllGapsMenuItem_actionPerformed();\r
+ else if(source==findMenuItem)\r
+ findMenuItem_actionPerformed();\r
+ else if(source==font)\r
+ new FontChooser(alignPanel);\r
+ else if (source == newView)\r
+ newView();\r
+ else if(source==showColumns)\r
+ {\r
+ viewport.showAllHiddenColumns(); alignPanel.repaint();\r
+ }\r
+ else if(source==showSeqs)\r
+ {\r
+ viewport.showAllHiddenSeqs();\r
+ }\r
+ else if(source == hideColumns)\r
+ {\r
+ viewport.hideSelectedColumns(); alignPanel.repaint();\r
+ }\r
+ else if(source == hideSequences && viewport.getSelectionGroup()!=null)\r
+ {\r
+ viewport.hideAllSelectedSeqs();\r
+ }\r
+ else if(source==featureSettings)\r
+ new FeatureSettings(alignPanel);\r
+ else if(source==overviewMenuItem)\r
+ overviewMenuItem_actionPerformed();\r
+ else if(source==noColourmenuItem)\r
+ changeColour(null);\r
+ else if(source==clustalColour)\r
+ {\r
+ abovePIDThreshold.setState(false);\r
+ changeColour(new ClustalxColourScheme(viewport.alignment.getSequences(),\r
+ viewport.alignment.getWidth()));\r
+ }\r
+ else if(source==zappoColour)\r
+ changeColour(new ZappoColourScheme());\r
+ else if(source==taylorColour)\r
+ changeColour(new TaylorColourScheme());\r
+ else if(source==hydrophobicityColour)\r
+ changeColour(new HydrophobicColourScheme());\r
+ else if(source==helixColour)\r
+ changeColour(new HelixColourScheme());\r
+ else if(source==strandColour)\r
+ changeColour(new StrandColourScheme());\r
+ else if(source==turnColour)\r
+ changeColour(new TurnColourScheme());\r
+ else if(source==buriedColour)\r
+ changeColour(new BuriedColourScheme());\r
+ else if(source==nucleotideColour)\r
+ changeColour(new NucleotideColourScheme());\r
+ else if(source==modifyPID)\r
+ modifyPID_actionPerformed();\r
+ else if(source==modifyConservation)\r
+ modifyConservation_actionPerformed();\r
+ else if(source==userDefinedColour)\r
+ new UserDefinedColours(alignPanel, null);\r
+ else if(source==PIDColour)\r
+ changeColour(new PIDColourScheme());\r
+ else if(source==BLOSUM62Colour)\r
+ changeColour(new Blosum62ColourScheme());\r
+ else if(source==annotationColour)\r
+ new AnnotationColourChooser(viewport, alignPanel);\r
+ else if(source==sortPairwiseMenuItem)\r
+ sortPairwiseMenuItem_actionPerformed();\r
+ else if(source==sortIDMenuItem)\r
+ sortIDMenuItem_actionPerformed();\r
+ else if(source==sortGroupMenuItem)\r
+ sortGroupMenuItem_actionPerformed();\r
+ else if(source==removeRedundancyMenuItem)\r
+ removeRedundancyMenuItem_actionPerformed();\r
+ else if(source==pairwiseAlignmentMenuItem)\r
+ pairwiseAlignmentMenuItem_actionPerformed();\r
+ else if(source==PCAMenuItem)\r
+ PCAMenuItem_actionPerformed();\r
+ else if(source==averageDistanceTreeMenuItem)\r
+ averageDistanceTreeMenuItem_actionPerformed();\r
+ else if(source==neighbourTreeMenuItem)\r
+ neighbourTreeMenuItem_actionPerformed();\r
+ else if(source==njTreeBlosumMenuItem)\r
+ njTreeBlosumMenuItem_actionPerformed();\r
+ else if(source==avDistanceTreeBlosumMenuItem)\r
+ avTreeBlosumMenuItem_actionPerformed();\r
+ else if(source==documentation)\r
+ documentation_actionPerformed();\r
+ else if(source==about)\r
+ about_actionPerformed();\r
+\r
+ }\r
+\r
+ public void inputText_actionPerformed()\r
+ {\r
+ CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);\r
+ Frame frame = new Frame();\r
+ frame.add(cap);\r
+ jalview.bin.JalviewLite.addFrame(frame, "Cut & Paste Input", 500, 500);\r
+ }\r
\r
protected void outputText_actionPerformed(ActionEvent e)\r
{\r
- CutAndPasteTransfer cap = new CutAndPasteTransfer(false);\r
- Frame frame = new Frame();\r
- frame.add(cap);\r
- jalview.bin.JalviewLite.addFrame(frame,"Alignment output - "+e.getActionCommand(),600, 500);\r
- cap.setText( FormatAdapter.formatSequences(e.getActionCommand(), viewport.getAlignment().getSequences()));\r
+ CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);\r
+ Frame frame = new Frame();\r
+ frame.add(cap);\r
+ jalview.bin.JalviewLite.addFrame(frame,\r
+ "Alignment output - " + e.getActionCommand(),\r
+ 600, 500);\r
+ cap.setText(new AppletFormatAdapter().formatSequences(e.getActionCommand(),\r
+ viewport.getAlignment().getSequences(),\r
+ viewport.showJVSuffix));\r
}\r
\r
- public void closeMenuItem_actionPerformed(ActionEvent e)\r
+ void launchFullApplication()\r
{\r
- dispose();\r
+ StringBuffer url = new StringBuffer(jalviewServletURL);\r
+\r
+ url.append("?open="+\r
+ appendProtocol( viewport.applet.getParameter("file") ) );\r
+\r
+ if(viewport.applet.getParameter("features")!=null)\r
+ {\r
+ url.append( "&features=" );\r
+ url.append( appendProtocol( viewport.applet.getParameter("features") ) );\r
+ }\r
+\r
+ if(viewport.applet.getParameter("annotations")!=null)\r
+ {\r
+ url.append( "&annotations=" );\r
+ url.append( appendProtocol( viewport.applet.getParameter("annotations") ) );\r
+ }\r
+\r
+ if(viewport.applet.getParameter("jnetfile")!=null)\r
+ {\r
+ url.append( "&annotations=" );\r
+ url.append( appendProtocol( viewport.applet.getParameter("jnetfile") ) );\r
+ }\r
+\r
+ if(viewport.applet.getParameter("defaultColour")!=null)\r
+ {\r
+ url.append("&colour=" +\r
+ removeWhiteSpace(viewport.applet.getParameter("defaultColour"))\r
+ );\r
+ }\r
+\r
+ if(viewport.applet.getParameter("userDefinedColour")!=null)\r
+ {\r
+ url.append( "&colour=" +\r
+ removeWhiteSpace( viewport.applet.getParameter("userDefinedColour") )\r
+ );\r
+ }\r
+\r
+ showURL(url.toString(), "FULL_APP");\r
}\r
\r
- Stack historyList = new Stack();\r
- Stack redoList = new Stack();\r
\r
+ String removeWhiteSpace(String colour)\r
+ {\r
+ StringBuffer sb = new StringBuffer();\r
+ for (int i = 0; i < colour.length(); i++)\r
+ {\r
+ if (Character.isWhitespace(colour.charAt(i)))\r
+ sb.append("%20");\r
+ else\r
+ sb.append(colour.charAt(i));\r
+ }\r
+\r
+ return sb.toString();\r
+ }\r
+\r
+\r
+ String appendProtocol(String url)\r
+ {\r
+ try{\r
+ new URL(url);\r
+ }catch(java.net.MalformedURLException ex)\r
+ {\r
+ url = viewport.applet.getCodeBase()+url;\r
+ }\r
+ return url;\r
+ }\r
+\r
+ public void closeMenuItem_actionPerformed()\r
+ {\r
+ PaintRefresher.RemoveComponent(alignPanel);\r
+ PaintRefresher.RemoveComponent(alignPanel.seqPanel.seqCanvas);\r
+ PaintRefresher.RemoveComponent(alignPanel.idPanel.idCanvas);\r
+\r
+ if(PaintRefresher.components.size()==0 && viewport.applet==null)\r
+ System.exit(0);\r
+\r
+ this.dispose();\r
+ }\r
+\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ */\r
void updateEditMenuBar()\r
{\r
- if(historyList.size()>0)\r
- {\r
- undoMenuItem.setEnabled(true);\r
- Object [] history = (Object[])historyList.elementAt(0);\r
- undoMenuItem.setLabel("Undo "+history[0]);\r
- }\r
+\r
+ if (viewport.historyList.size() > 0)\r
+ {\r
+ undoMenuItem.setEnabled(true);\r
+ CommandI command = (CommandI) viewport.historyList.peek();\r
+ undoMenuItem.setLabel("Undo " + command.getDescription());\r
+ }\r
else\r
{\r
undoMenuItem.setEnabled(false);\r
undoMenuItem.setLabel("Undo");\r
}\r
\r
- if(redoList.size()>0)\r
- {\r
- redoMenuItem.setEnabled(true);\r
- Object [] history = (Object[])redoList.elementAt(0);\r
- redoMenuItem.setLabel("Redo "+history[0]);\r
- }\r
+ if (viewport.redoList.size() > 0)\r
+ {\r
+ redoMenuItem.setEnabled(true);\r
+\r
+ CommandI command = (CommandI) viewport.redoList.peek();\r
+ redoMenuItem.setLabel("Redo " + command.getDescription());\r
+ }\r
else\r
{\r
redoMenuItem.setEnabled(false);\r
}\r
}\r
\r
- public void addHistoryItem(String type)\r
+ public void addHistoryItem(CommandI command)\r
{\r
- // must make sure we add new sequence objects her, not refs to the existing sequences\r
- redoList.removeAllElements();\r
- SequenceI[] seq = new SequenceI[viewport.getAlignment().getHeight()];\r
- for(int i=0; i<viewport.getAlignment().getHeight(); i++)\r
+ if(command.getSize()>0)\r
{\r
- seq[i] = new Sequence( viewport.getAlignment().getSequenceAt(i).getName(),\r
- viewport.getAlignment().getSequenceAt(i).getSequence());\r
+ viewport.historyList.push(command);\r
+ viewport.redoList.removeAllElements();\r
+ updateEditMenuBar();\r
+ viewport.hasHiddenColumns = viewport.colSel.getHiddenColumns() != null;\r
}\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param e DOCUMENT ME!\r
+ */\r
+ protected void undoMenuItem_actionPerformed()\r
+ {\r
+ if(viewport.historyList.size()<1)\r
+ return;\r
+\r
+ CommandI command = (CommandI)viewport.historyList.pop();\r
+ viewport.redoList.push(command);\r
+ command.undoCommand();\r
+\r
+ AlignViewport originalSource = getOriginatingSource(command);\r
\r
- historyList.addElement(new Object[]{type, seq} );\r
+ originalSource.hasHiddenColumns = viewport.colSel.getHiddenColumns() != null;\r
updateEditMenuBar();\r
+ originalSource.firePropertyChange("alignment", null,null);\r
}\r
\r
- protected void undoMenuItem_actionPerformed(ActionEvent e)\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param e DOCUMENT ME!\r
+ */\r
+ protected void redoMenuItem_actionPerformed()\r
{\r
- Object [] history = (Object[])historyList.elementAt(0);\r
- historyList.removeElementAt(0);\r
- // add the redo state before continuing!!\r
- SequenceI[] seq = new SequenceI[viewport.getAlignment().getHeight()];\r
- for (int i = 0; i < viewport.getAlignment().getHeight(); i++)\r
- {\r
- seq[i] = new Sequence(viewport.getAlignment().getSequenceAt(i).getName(),\r
- viewport.getAlignment().getSequenceAt(i).\r
- getSequence());\r
- }\r
- /////////\r
+ if(viewport.redoList.size()<1)\r
+ return;\r
\r
- redoList.addElement(new Object[] {history[0], seq});\r
+ CommandI command = (CommandI) viewport.redoList.pop();\r
+ viewport.historyList.push(command);\r
+ command.doCommand();\r
\r
- seq = (SequenceI[]) history[1];\r
+ AlignViewport originalSource = getOriginatingSource(command);\r
+ originalSource.hasHiddenColumns = viewport.colSel.getHiddenColumns()!=null;\r
\r
- AlignmentAnnotation[] old = viewport.alignment.getAlignmentAnnotation();\r
- viewport.setAlignment(new Alignment(seq));\r
- updateEditMenuBar();\r
- for (int i = 0; i < old.length; i++)\r
- viewport.alignment.addAnnotation(old[i]);\r
+ updateEditMenuBar();\r
+ originalSource.firePropertyChange("alignment", null, null);\r
+ }\r
\r
- viewport.updateConservation();\r
- viewport.updateConsensus();\r
- alignPanel.repaint();\r
+ AlignViewport getOriginatingSource(CommandI command)\r
+ {\r
+ AlignViewport originalSource = null;\r
+ //For sequence removal and addition, we need to fire\r
+ //the property change event FROM the viewport where the\r
+ //original alignment was altered\r
+ if (command instanceof EditCommand)\r
+ {\r
+ EditCommand editCommand = (EditCommand) command;\r
+ AlignmentI al = editCommand.getAlignment();\r
+ Vector comps = (Vector) PaintRefresher.components\r
+ .get(viewport.getSequenceSetId());\r
+ for (int i = 0; i < comps.size(); i++)\r
+ {\r
+ if (comps.elementAt(i) instanceof AlignmentPanel)\r
+ {\r
+ if (al == ( (AlignmentPanel) comps.elementAt(i)).av.alignment)\r
+ {\r
+ originalSource = ( (AlignmentPanel) comps.elementAt(i)).av;\r
+ break;\r
+ }\r
+ }\r
+ }\r
+ if (originalSource == null && al!=null)\r
+ {\r
+ //The original view is closed, we must validate\r
+ //the current view against the closed view first\r
+ PaintRefresher.validateSequences(al, viewport.alignment);\r
+ originalSource = viewport;\r
+ }\r
+\r
+ }\r
+\r
+ return originalSource;\r
}\r
\r
public void moveSelectedSequences(boolean up)\r
{\r
SequenceGroup sg = viewport.getSelectionGroup();\r
if (sg == null)\r
+ {\r
return;\r
+ }\r
\r
if (up)\r
{\r
for (int i = 1; i < viewport.alignment.getHeight(); i++)\r
{\r
SequenceI seq = viewport.alignment.getSequenceAt(i);\r
- if (!sg.sequences.contains(seq))\r
+ if (!sg.getSequences(false).contains(seq))\r
+ {\r
continue;\r
+ }\r
\r
SequenceI temp = viewport.alignment.getSequenceAt(i - 1);\r
- if (sg.sequences.contains(temp))\r
+ if (sg.getSequences(false).contains(temp))\r
+ {\r
continue;\r
+ }\r
\r
viewport.alignment.getSequences().setElementAt(temp, i);\r
viewport.alignment.getSequences().setElementAt(seq, i - 1);\r
for (int i = viewport.alignment.getHeight() - 2; i > -1; i--)\r
{\r
SequenceI seq = viewport.alignment.getSequenceAt(i);\r
- if (!sg.sequences.contains(seq))\r
+ if (!sg.getSequences(true).contains(seq))\r
+ {\r
continue;\r
+ }\r
\r
SequenceI temp = viewport.alignment.getSequenceAt(i + 1);\r
- if (sg.sequences.contains(temp))\r
+ if (sg.getSequences(true).contains(temp))\r
+ {\r
continue;\r
+ }\r
\r
viewport.alignment.getSequences().setElementAt(temp, i);\r
viewport.alignment.getSequences().setElementAt(seq, i + 1);\r
alignPanel.repaint();\r
}\r
\r
-\r
- StringBuffer copiedSequences;\r
- protected void copy_actionPerformed(ActionEvent e)\r
+ static StringBuffer copiedSequences;\r
+ static Vector copiedHiddenColumns;\r
+ protected void copy_actionPerformed()\r
{\r
- if(viewport.getSelectionGroup()==null)\r
- return;\r
+ if (viewport.getSelectionGroup() == null)\r
+ {\r
+ return;\r
+ }\r
\r
- SequenceGroup sg = viewport.getSelectionGroup();\r
- copiedSequences = new StringBuffer();\r
- Hashtable orderedSeqs = new Hashtable();\r
- for(int i=0; i<sg.getSize(); i++)\r
- {\r
+ SequenceGroup sg = viewport.getSelectionGroup();\r
+ copiedSequences = new StringBuffer();\r
+ Hashtable orderedSeqs = new Hashtable();\r
+ for (int i = 0; i < sg.getSize(false); i++)\r
+ {\r
SequenceI seq = sg.getSequenceAt(i);\r
int index = viewport.alignment.findIndex(seq);\r
- orderedSeqs.put(index+"", seq);\r
- }\r
+ orderedSeqs.put(index + "", seq);\r
+ }\r
\r
- int index=0;\r
- for(int i=0; i<sg.getSize(); i++)\r
- {\r
- SequenceI seq = null;\r
- while( seq == null )\r
- {\r
- if(orderedSeqs.containsKey(index+""))\r
- {\r
- seq = (SequenceI) orderedSeqs.get(index + "");\r
- index++;\r
- break;\r
- }\r
- else\r
- index++;\r
- }\r
+ int index = 0, startRes, endRes;\r
+ char ch;\r
\r
- copiedSequences.append( seq.getName()+"\t"+seq.findPosition( sg.getStartRes() ) +"\t"\r
- +seq.findPosition( sg.getEndRes() )+ "\t"\r
- +sg.getSequenceAt(i).getSequence(sg.getStartRes(), sg.getEndRes()+1)+"\n");\r
- }\r
+ if (viewport.hasHiddenColumns && viewport.getSelectionGroup() != null)\r
+ {\r
+ copiedHiddenColumns = new Vector();\r
+ int hiddenOffset = viewport.getSelectionGroup().getStartRes();\r
+ for (int i = 0; i < viewport.getColumnSelection().getHiddenColumns().size();\r
+ i++)\r
+ {\r
+ int[] region = (int[])\r
+ viewport.getColumnSelection().getHiddenColumns().elementAt(i);\r
+\r
+ copiedHiddenColumns.addElement(new int[]\r
+ {region[0] - hiddenOffset,\r
+ region[1] - hiddenOffset});\r
+ }\r
+ }\r
+ else\r
+ copiedHiddenColumns = null;\r
\r
- }\r
\r
+ for (int i = 0; i < sg.getSize(false); i++)\r
+ {\r
+ SequenceI seq = null;\r
+\r
+ while (seq == null)\r
+ {\r
+ if (orderedSeqs.containsKey(index + ""))\r
+ {\r
+ seq = (SequenceI) orderedSeqs.get(index + "");\r
+ index++;\r
+\r
+ break;\r
+ }\r
+ else\r
+ {\r
+ index++;\r
+ }\r
+ }\r
+\r
+ //FIND START RES\r
+ //Returns residue following index if gap\r
+ startRes = seq.findPosition(sg.getStartRes());\r
+\r
+ //FIND END RES\r
+ //Need to find the residue preceeding index if gap\r
+ endRes = 0;\r
\r
- protected void pasteNew_actionPerformed(ActionEvent e)\r
+ for (int j = 0; j < sg.getEndRes()+1 && j < seq.getLength(); j++)\r
+ {\r
+ ch = seq.getCharAt(j);\r
+ if (!jalview.util.Comparison.isGap( (ch)))\r
+ {\r
+ endRes++;\r
+ }\r
+ }\r
+\r
+ if(endRes>0)\r
+ {\r
+ endRes += seq.getStart() -1;\r
+ }\r
+\r
+ copiedSequences.append(seq.getName() + "\t" +\r
+ startRes + "\t" +\r
+ endRes + "\t" +\r
+ seq.getSequence(sg.getStartRes(),\r
+ sg.getEndRes() + 1) + "\n");\r
+ }\r
+\r
+ }\r
+\r
+ protected void pasteNew_actionPerformed()\r
{\r
paste(true);\r
}\r
\r
- protected void pasteThis_actionPerformed(ActionEvent e)\r
+ protected void pasteThis_actionPerformed()\r
{\r
- addHistoryItem("Paste");\r
paste(false);\r
}\r
\r
void paste(boolean newAlignment)\r
{\r
- try{\r
+ try\r
+ {\r
+\r
if (copiedSequences == null)\r
+ {\r
return;\r
+ }\r
\r
StringTokenizer st = new StringTokenizer(copiedSequences.toString());\r
Vector seqs = new Vector();\r
String name = st.nextToken();\r
int start = Integer.parseInt(st.nextToken());\r
int end = Integer.parseInt(st.nextToken());\r
- Sequence sequence = new Sequence(name,st.nextToken(), start, end);\r
-\r
- if(!newAlignment)\r
- viewport.alignment.addSequence(sequence);\r
- else\r
- seqs.addElement(sequence);\r
+ seqs.addElement(new Sequence(name, st.nextToken(), start, end));\r
}\r
-\r
- if(newAlignment)\r
+ SequenceI[] newSeqs = new SequenceI[seqs.size()];\r
+ for (int i = 0; i < seqs.size(); i++)\r
{\r
- SequenceI[] newSeqs = new SequenceI[seqs.size()];\r
- for(int i=0; i<seqs.size(); i++)\r
- newSeqs[i] = (SequenceI)seqs.elementAt(i);\r
+ newSeqs[i] = (SequenceI) seqs.elementAt(i);\r
+ }\r
\r
- AlignFrame af = new AlignFrame(new Alignment(newSeqs), applet);\r
+ if (newAlignment)\r
+ {\r
String newtitle = new String("Copied sequences");\r
- if( getTitle().startsWith("Copied sequences"))\r
- newtitle = getTitle();\r
- else\r
- newtitle = newtitle.concat("- from "+getTitle());\r
- jalview.bin.JalviewLite.addFrame(af, newtitle, NEW_WINDOW_WIDTH, NEW_WINDOW_HEIGHT);\r
+ if (getTitle().startsWith("Copied sequences"))\r
+ {\r
+ newtitle = getTitle();\r
+ }\r
+ else\r
+ {\r
+ newtitle = newtitle.concat("- from " + getTitle());\r
+ }\r
+ AlignFrame af = new AlignFrame(new Alignment(newSeqs),\r
+ viewport.applet,\r
+ newtitle,\r
+ false);\r
+ if (copiedHiddenColumns != null)\r
+ {\r
+ for (int i = 0; i < copiedHiddenColumns.size(); i++)\r
+ {\r
+ int[] region = (int[]) copiedHiddenColumns.elementAt(i);\r
+ af.viewport.hideColumns(region[0], region[1]);\r
+ }\r
+ }\r
+\r
+\r
+ jalview.bin.JalviewLite.addFrame(af, newtitle, DEFAULT_WIDTH,\r
+ DEFAULT_HEIGHT);\r
}\r
else\r
{\r
+ for (int i = 0; i < newSeqs.length; i++)\r
+ {\r
+ viewport.alignment.addSequence(newSeqs[i]);\r
+ }\r
+\r
+ //!newAlignment\r
+ addHistoryItem(new EditCommand(\r
+ "Add sequences",\r
+ EditCommand.PASTE,\r
+ newSeqs,\r
+ 0,\r
+ viewport.alignment.getWidth(),\r
+ viewport.alignment)\r
+ );\r
+\r
viewport.setEndSeq(viewport.alignment.getHeight());\r
viewport.alignment.getWidth();\r
- viewport.updateConservation();\r
- viewport.updateConsensus();\r
- alignPanel.repaint();\r
+ viewport.firePropertyChange("alignment", null, null);\r
}\r
\r
- }catch(Exception ex){}// could be anything being pasted in here\r
+ }\r
+ catch (Exception ex)\r
+ {} // could be anything being pasted in here\r
\r
}\r
\r
-\r
- protected void cut_actionPerformed(ActionEvent e)\r
+ protected void cut_actionPerformed()\r
{\r
- copy_actionPerformed(null);\r
- delete_actionPerformed(null);\r
+ copy_actionPerformed();\r
+ delete_actionPerformed();\r
}\r
\r
- protected void delete_actionPerformed(ActionEvent e)\r
+ protected void delete_actionPerformed()\r
{\r
- addHistoryItem("Delete");\r
- if (viewport.getSelectionGroup() == null)\r
+\r
+ SequenceGroup sg = viewport.getSelectionGroup();\r
+ if (sg == null)\r
+ {\r
return;\r
+ }\r
\r
- SequenceGroup sg = viewport.getSelectionGroup();\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
- seq.deleteChars(sg.getStartRes(), sg.getEndRes()+1);\r
+ Vector seqs = new Vector();\r
+ SequenceI seq;\r
+ for (int i = 0; i < sg.getSize(false); i++)\r
+ {\r
+ seq = sg.getSequenceAt(i);\r
+ seqs.addElement(seq);\r
+ }\r
\r
- if(seq.getSequence().length()<1)\r
- viewport.getAlignment().deleteSequence(seq);\r
- else\r
- viewport.getAlignment().getSequences().setElementAt(seq, index);\r
- }\r
\r
- viewport.setSelectionGroup(null);\r
- viewport.alignment.deleteGroup(sg);\r
- viewport.resetSeqLimits( alignPanel.seqPanel.seqCanvas.getSize().height);\r
- if(viewport.getAlignment().getHeight()<1)\r
- try\r
- {\r
- this.setVisible(false);\r
- }catch(Exception ex){}\r
- viewport.updateConservation();\r
- viewport.updateConsensus();\r
- alignPanel.repaint();\r
+ // If the cut affects all sequences, remove highlighted columns\r
+ if (sg.getSize(false) == viewport.alignment.getHeight())\r
+ {\r
+ viewport.getColumnSelection().removeElements(sg.getStartRes(),\r
+ sg.getEndRes() + 1);\r
+ }\r
\r
- }\r
\r
+ SequenceI [] cut = new SequenceI[seqs.size()];\r
+ for(int i=0; i<seqs.size(); i++)\r
+ cut[i] = (SequenceI)seqs.elementAt(i);\r
\r
\r
- protected void redoMenuItem_actionPerformed(ActionEvent e)\r
- {\r
- Object [] history = (Object[])redoList.pop();\r
- SequenceI[] seq = (SequenceI[]) history[1];\r
-\r
- AlignmentAnnotation[] old = viewport.alignment.getAlignmentAnnotation();\r
- viewport.setAlignment(new Alignment(seq));\r
- for (int i = 0; i < old.length; i++)\r
- viewport.alignment.addAnnotation(old[i]);\r
-\r
- viewport.updateConservation();\r
- viewport.updateConsensus();\r
- updateEditMenuBar();\r
- alignPanel.repaint();\r
- }\r
+ /*\r
+ //ADD HISTORY ITEM\r
+ */\r
+ addHistoryItem(new EditCommand("Cut Sequences",\r
+ EditCommand.CUT,\r
+ cut,\r
+ sg.getStartRes(),\r
+ sg.getEndRes()-sg.getStartRes()+1,\r
+ viewport.alignment));\r
+\r
+\r
+ viewport.setSelectionGroup(null);\r
+ viewport.alignment.deleteGroup(sg);\r
+\r
+ viewport.firePropertyChange("alignment", null,\r
+ viewport.getAlignment().getSequences());\r
\r
+ if (viewport.getAlignment().getHeight() < 1)\r
+ {\r
+ this.setVisible(false);\r
+ }\r
+ }\r
\r
- protected void deleteGroups_actionPerformed(ActionEvent e)\r
+ protected void deleteGroups_actionPerformed()\r
{\r
viewport.alignment.deleteAllGroups();\r
+ viewport.sequenceColours=null;\r
viewport.setSelectionGroup(null);\r
\r
alignPanel.repaint();\r
}\r
\r
-\r
-\r
- public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)\r
+ public void selectAllSequenceMenuItem_actionPerformed()\r
{\r
SequenceGroup sg = new SequenceGroup();\r
- for (int i=0; i<viewport.getAlignment().getSequences().size(); i++)\r
- sg.addSequence( viewport.getAlignment().getSequenceAt(i));\r
- sg.setEndRes(viewport.alignment.getWidth());\r
+ for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)\r
+ {\r
+ sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);\r
+ }\r
+ sg.setEndRes(viewport.alignment.getWidth()-1);\r
viewport.setSelectionGroup(sg);\r
alignPanel.repaint();\r
- PaintRefresher.Refresh(null);\r
+ PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());\r
}\r
\r
- public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)\r
+ public void deselectAllSequenceMenuItem_actionPerformed()\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
- PaintRefresher.Refresh(null);\r
+ alignPanel.idPanel.idCanvas.searchResults = null;\r
+ alignPanel.seqPanel.seqCanvas.highlightSearchResults(null);\r
+ alignPanel.repaint();\r
+ PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());\r
}\r
\r
- public void invertSequenceMenuItem_actionPerformed(ActionEvent e)\r
+ public void invertSequenceMenuItem_actionPerformed()\r
{\r
SequenceGroup sg = viewport.getSelectionGroup();\r
- for (int i=0; i<viewport.getAlignment().getSequences().size(); i++)\r
- sg.addOrRemove (viewport.getAlignment().getSequenceAt(i));\r
+ for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)\r
+ {\r
+ sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);\r
+ }\r
\r
- PaintRefresher.Refresh(null);\r
+ PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());\r
}\r
\r
- public void remove2LeftMenuItem_actionPerformed(ActionEvent e)\r
+ void trimAlignment(boolean trimLeft)\r
{\r
- addHistoryItem("delete columns");\r
ColumnSelection colSel = viewport.getColumnSelection();\r
+ int column;\r
+\r
if (colSel.size() > 0)\r
{\r
- int min = colSel.getMin();\r
- viewport.getAlignment().trimLeft(min);\r
- colSel.compensateForEdit(0,min);\r
+ if(trimLeft)\r
+ column = colSel.getMin();\r
+ else\r
+ column = colSel.getMax();\r
\r
+ SequenceI [] seqs;\r
if(viewport.getSelectionGroup()!=null)\r
- viewport.getSelectionGroup().adjustForRemoveLeft(min);\r
+ seqs = viewport.getSelectionGroup().getSequencesAsArray(true);\r
+ else\r
+ seqs = viewport.alignment.getSequencesArray();\r
+\r
+\r
+ TrimRegionCommand trimRegion;\r
+ if(trimLeft)\r
+ {\r
+ trimRegion = new TrimRegionCommand("Remove Left",\r
+ TrimRegionCommand.TRIM_LEFT,\r
+ seqs,\r
+ column,\r
+ viewport.alignment,\r
+ viewport.colSel,\r
+ viewport.selectionGroup);\r
+ viewport.setStartRes(0);\r
+ }\r
+ else\r
+ {\r
+ trimRegion = new TrimRegionCommand("Remove Right",\r
+ TrimRegionCommand.TRIM_RIGHT,\r
+ seqs,\r
+ column,\r
+ viewport.alignment,\r
+ viewport.colSel,\r
+ viewport.selectionGroup);\r
+ }\r
+\r
+ statusBar.setText("Removed "+trimRegion.getSize()+" columns.");\r
+\r
+\r
+ addHistoryItem(trimRegion);\r
\r
Vector groups = viewport.alignment.getGroups();\r
- for(int i=0; i<groups.size(); i++)\r
+\r
+ for (int i = 0; i < groups.size(); i++)\r
{\r
SequenceGroup sg = (SequenceGroup) groups.elementAt(i);\r
- if(!sg.adjustForRemoveLeft(min))\r
+\r
+ if ( (trimLeft && !sg.adjustForRemoveLeft(column))\r
+ || (!trimLeft && !sg.adjustForRemoveRight(column)))\r
+ {\r
viewport.alignment.deleteGroup(sg);\r
+ }\r
}\r
\r
- alignPanel.repaint();\r
+ viewport.firePropertyChange("alignment", null,\r
+ viewport.getAlignment().getSequences());\r
}\r
}\r
\r
- public void remove2RightMenuItem_actionPerformed(ActionEvent e)\r
+\r
+ public void removeGappedColumnMenuItem_actionPerformed()\r
{\r
- addHistoryItem("delete columns");\r
- ColumnSelection colSel = viewport.getColumnSelection();\r
- if (colSel.size() > 0)\r
- {\r
- int max = colSel.getMax();\r
- viewport.getAlignment().trimRight(max);\r
- if(viewport.getSelectionGroup()!=null)\r
- viewport.getSelectionGroup().adjustForRemoveRight(max);\r
+ int start = 0, end = viewport.alignment.getWidth()-1;\r
\r
- Vector groups = viewport.alignment.getGroups();\r
- for(int i=0; i<groups.size(); i++)\r
- {\r
- SequenceGroup sg = (SequenceGroup) groups.elementAt(i);\r
- if(!sg.adjustForRemoveRight(max))\r
- viewport.alignment.deleteGroup(sg);\r
- }\r
+ SequenceI[] seqs;\r
+ if (viewport.getSelectionGroup() != null)\r
+ {\r
+ seqs = viewport.getSelectionGroup().getSequencesAsArray(true);\r
+ start = viewport.getSelectionGroup().getStartRes();\r
+ end = viewport.getSelectionGroup().getEndRes();\r
+ }\r
+ else\r
+ seqs = viewport.alignment.getSequencesArray();\r
\r
\r
+ RemoveGapColCommand removeGapCols =\r
+ new RemoveGapColCommand("Remove Gapped Columns",\r
+ seqs,\r
+ start, end,\r
+ viewport.getGapCharacter());\r
\r
- alignPanel.repaint();\r
- }\r
+ addHistoryItem(removeGapCols);\r
\r
- }\r
+ statusBar.setText("Removed "+removeGapCols.getSize()+" empty columns.");\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
+ // ShiftList shifts;\r
+ // viewport.getAlignment().removeGaps(shifts=new ShiftList());\r
+ // edit.alColumnChanges=shifts.getInverse();\r
+ // if (viewport.hasHiddenColumns)\r
+ // viewport.getColumnSelection().compensateForEdits(shifts);\r
+ viewport.setStartRes(seq.findIndex(startRes)-1);\r
+ viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());\r
\r
- public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)\r
- {\r
- addHistoryItem("delete gapped columns");\r
- viewport.getAlignment().removeGaps();\r
- viewport.updateConservation();\r
- viewport.updateConsensus();\r
- alignPanel.repaint();\r
}\r
\r
- public void removeAllGapsMenuItem_actionPerformed(ActionEvent e)\r
+ public void removeAllGapsMenuItem_actionPerformed()\r
{\r
- addHistoryItem("delete all gaps");\r
- SequenceI current;\r
- int jSize;\r
- for (int i=0; i < viewport.getAlignment().getSequences().size();i++)\r
- {\r
- current = viewport.getAlignment().getSequenceAt(i);\r
- jSize = current.getLength();\r
- for (int j=0; j < jSize; j++)\r
- if(jalview.util.Comparison.isGap(current.getCharAt(j)))\r
- {\r
- current.deleteCharAt(j);\r
- j--;\r
- jSize--;\r
- }\r
+ int start = 0, end = viewport.alignment.getWidth()-1;\r
+\r
+ SequenceI[] seqs;\r
+ if (viewport.getSelectionGroup() != null)\r
+ {\r
+ seqs = viewport.getSelectionGroup().getSequencesAsArray(true);\r
+ start = viewport.getSelectionGroup().getStartRes();\r
+ end = viewport.getSelectionGroup().getEndRes();\r
}\r
- viewport.updateConservation();\r
- viewport.updateConsensus();\r
- alignPanel.repaint();\r
- }\r
+ else\r
+ seqs = viewport.alignment.getSequencesArray();\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
- public void findMenuItem_actionPerformed(ActionEvent e)\r
- {\r
- Finder finder = new Finder(alignPanel);\r
- }\r
+ addHistoryItem(new RemoveGapsCommand("Remove Gaps",\r
+ seqs,\r
+ start, end,\r
+ viewport.getGapCharacter()));\r
\r
+ viewport.setStartRes(seq.findIndex(startRes)-1);\r
\r
- public void font_actionPerformed(ActionEvent e)\r
- {\r
- Frame frame = new Frame();\r
- FontChooser fc = new FontChooser( alignPanel, frame);\r
- frame.add(fc);\r
- jalview.bin.JalviewLite.addFrame(frame, "Change Font", 440,100);\r
+ viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());\r
\r
}\r
\r
- protected void fullSeqId_actionPerformed(ActionEvent e)\r
+ public void findMenuItem_actionPerformed()\r
{\r
- viewport.setShowFullId( fullSeqId.getState() );\r
- alignPanel.idPanel.idCanvas.setSize( alignPanel.calculateIdWidth() );\r
- alignPanel.repaint();\r
+ new Finder(alignPanel);\r
}\r
\r
- protected void colourTextMenuItem_actionPerformed(ActionEvent e)\r
+ public void newView()\r
{\r
- viewport.setColourText( colourTextMenuItem.getState() );\r
- alignPanel.repaint();\r
- }\r
+ AlignmentI newal;\r
+ if (viewport.hasHiddenRows)\r
+ newal = new Alignment(viewport.getAlignment().\r
+ getHiddenSequences()\r
+ .getFullAlignment().\r
+ getSequencesArray());\r
+ else\r
+ newal = new Alignment(viewport.alignment.getSequencesArray());\r
+\r
+ AlignFrame newaf = new AlignFrame(newal,\r
+ viewport.applet,\r
+ "",\r
+ false);\r
+\r
+ newaf.viewport.sequenceSetID = alignPanel.av.getSequenceSetId();\r
+ PaintRefresher.Register(alignPanel, alignPanel.av.getSequenceSetId());\r
+ PaintRefresher.Register(newaf.alignPanel,\r
+ newaf.alignPanel.av.getSequenceSetId());\r
+\r
+ PaintRefresher.Register(newaf.alignPanel.idPanel.idCanvas,\r
+ newaf.alignPanel.av.getSequenceSetId());\r
+ PaintRefresher.Register(newaf.alignPanel.seqPanel.seqCanvas,\r
+ newaf.alignPanel.av.getSequenceSetId());\r
+\r
+ Vector comps = (Vector)PaintRefresher.components.get(viewport.getSequenceSetId());\r
+ int viewSize = -1;\r
+ for (int i = 0; i < comps.size(); i++)\r
+ {\r
+ if (comps.elementAt(i) instanceof AlignmentPanel)\r
+ viewSize++;\r
+ }\r
\r
- protected void wrapMenuItem_actionPerformed(ActionEvent e)\r
- {\r
- viewport.setWrapAlignment( wrapMenuItem.getState() );\r
- alignPanel.setWrapAlignment( wrapMenuItem.getState() );\r
- scaleAbove.setEnabled( wrapMenuItem.getState() );\r
- scaleLeft.setEnabled( wrapMenuItem.getState());\r
- scaleRight.setEnabled( wrapMenuItem.getState());\r
- alignPanel.repaint();\r
- }\r
+ String title = new String(this.getTitle());\r
+ if (title.indexOf("(View") > -1)\r
+ title = title.substring(0, title.indexOf("(View"));\r
\r
- protected void scaleAbove_actionPerformed(ActionEvent e)\r
- {\r
- viewport.setScaleAboveWrapped(scaleAbove.getState());\r
- alignPanel.repaint();\r
- }\r
+ title+= "(View "+viewSize+")";\r
\r
- protected void scaleLeft_actionPerformed(ActionEvent e)\r
- {\r
- viewport.setScaleLeftWrapped(scaleLeft.getState());\r
- alignPanel.repaint();\r
- }\r
+ newaf.setTitle(title.toString());\r
\r
- protected void scaleRight_actionPerformed(ActionEvent e)\r
- {\r
- viewport.setScaleRightWrapped(scaleRight.getState());\r
- alignPanel.repaint();\r
- }\r
\r
+ newaf.viewport.historyList = viewport.historyList;\r
+ newaf.viewport.redoList = viewport.redoList;\r
+\r
+ }\r
\r
\r
- public void viewBoxesMenuItem_actionPerformed(ActionEvent e)\r
+ public void seqLimits_itemStateChanged()\r
{\r
- viewport.setShowBoxes( viewBoxesMenuItem.getState() );\r
+ viewport.setShowJVSuffix(seqLimits.getState());\r
+ alignPanel.fontChanged();\r
alignPanel.repaint();\r
}\r
\r
- public void viewTextMenuItem_actionPerformed(ActionEvent e)\r
+\r
+ protected void colourTextMenuItem_actionPerformed()\r
{\r
- viewport.setShowText( viewTextMenuItem.getState() );\r
+ viewport.setColourText(colourTextMenuItem.getState());\r
alignPanel.repaint();\r
}\r
\r
-\r
- protected void renderGapsMenuItem_actionPerformed(ActionEvent e)\r
+ protected void wrapMenuItem_actionPerformed()\r
{\r
- viewport.setRenderGaps(renderGapsMenuItem.getState());\r
+ viewport.setWrapAlignment(wrapMenuItem.getState());\r
+ alignPanel.setWrapAlignment(wrapMenuItem.getState());\r
+ scaleAbove.setEnabled(wrapMenuItem.getState());\r
+ scaleLeft.setEnabled(wrapMenuItem.getState());\r
+ scaleRight.setEnabled(wrapMenuItem.getState());\r
alignPanel.repaint();\r
}\r
\r
\r
- public void annotationPanelMenuItem_actionPerformed(ActionEvent e)\r
+ public void overviewMenuItem_actionPerformed()\r
{\r
- if(annotationPanelMenuItem.getState() && viewport.getWrapAlignment())\r
+ if (alignPanel.overviewPanel != null)\r
{\r
- annotationPanelMenuItem.setState(false);\r
return;\r
}\r
- viewport.setShowAnnotation( annotationPanelMenuItem.getState() );\r
- alignPanel.setAnnotationVisible( annotationPanelMenuItem.getState() );\r
- }\r
-\r
- public void overviewMenuItem_actionPerformed(ActionEvent e)\r
- {\r
- if (alignPanel.overviewPanel != null)\r
- return;\r
\r
Frame frame = new Frame();\r
OverviewPanel overview = new OverviewPanel(alignPanel);\r
frame.add(overview);\r
// +50 must allow for applet frame window\r
jalview.bin.JalviewLite.addFrame(frame, "Overview " + this.getTitle(),\r
- overview.preferredSize().width, overview.preferredSize().height+50);\r
+ overview.preferredSize().width,\r
+ overview.preferredSize().height + 50);\r
\r
frame.pack();\r
frame.addWindowListener(new WindowAdapter()\r
- { public void windowClosing(WindowEvent e)\r
+ {\r
+ public void windowClosing(WindowEvent e)\r
{\r
- alignPanel.setOverviewPanel(null);\r
+ alignPanel.setOverviewPanel(null);\r
};\r
});\r
\r
- alignPanel.setOverviewPanel( overview );\r
-\r
-\r
- }\r
-\r
- protected void noColourmenuItem_actionPerformed(ActionEvent e)\r
- {\r
- changeColour( null );\r
- }\r
-\r
-\r
- public void clustalColour_actionPerformed(ActionEvent e)\r
- {\r
- abovePIDThreshold.setState(false);\r
- changeColour(new ClustalxColourScheme(viewport.alignment.getSequences(), viewport.alignment.getWidth()));\r
- }\r
-\r
- public void zappoColour_actionPerformed(ActionEvent e)\r
- {\r
- changeColour(new ZappoColourScheme());\r
- }\r
-\r
- public void taylorColour_actionPerformed(ActionEvent e)\r
- {\r
- changeColour(new TaylorColourScheme());\r
- }\r
-\r
-\r
- public void hydrophobicityColour_actionPerformed(ActionEvent e)\r
- {\r
- changeColour( new HydrophobicColourScheme() );\r
- }\r
-\r
- public void helixColour_actionPerformed(ActionEvent e)\r
- {\r
- changeColour(new HelixColourScheme() );\r
- }\r
-\r
-\r
- public void strandColour_actionPerformed(ActionEvent e)\r
- {\r
- changeColour(new StrandColourScheme());\r
- }\r
-\r
-\r
- public void turnColour_actionPerformed(ActionEvent e)\r
- {\r
- changeColour(new TurnColourScheme());\r
- }\r
-\r
+ alignPanel.setOverviewPanel(overview);\r
\r
- public void buriedColour_actionPerformed(ActionEvent e)\r
- {\r
- changeColour(new BuriedColourScheme() );\r
- }\r
-\r
- public void nucleotideColour_actionPerformed(ActionEvent e)\r
- {\r
- changeColour(new NucleotideColourScheme());\r
- }\r
-\r
-\r
- protected void applyToAllGroups_actionPerformed(ActionEvent e)\r
- {\r
- viewport.setColourAppliesToAllGroups(applyToAllGroups.getState());\r
}\r
\r
\r
-\r
void changeColour(ColourSchemeI cs)\r
{\r
int threshold = 0;\r
\r
- if ( viewport.getAbovePIDThreshold() )\r
+ if(cs!=null)\r
{\r
- threshold = SliderPanel.setPIDSliderSource(alignPanel, cs, "Background");\r
-\r
- if (cs instanceof ResidueColourScheme)\r
- ( (ResidueColourScheme) cs).setThreshold(threshold);\r
- else if (cs instanceof ScoreColourScheme)\r
- ( (ScoreColourScheme) cs).setThreshold(threshold);\r
+ if (viewport.getAbovePIDThreshold())\r
+ {\r
+ threshold = SliderPanel.setPIDSliderSource(alignPanel, cs, "Background");\r
\r
- viewport.setGlobalColourScheme(cs);\r
- }\r
- else if (cs instanceof ResidueColourScheme)\r
- ( (ResidueColourScheme) cs).setThreshold(0);\r
- else if (cs instanceof ScoreColourScheme)\r
- ( (ScoreColourScheme) cs).setThreshold(0);\r
+ cs.setThreshold(threshold, 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
- if (viewport.getConservationSelected())\r
- {\r
- ConservationColourScheme ccs = null;\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
- 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
- c.calculate();\r
- c.verdict(false, viewport.ConsPercGaps);\r
+ cs.setConservation(c);\r
\r
- ccs = new ConservationColourScheme(c, cs);\r
+ cs.setConservationInc(SliderPanel.setConservationSlider(alignPanel, cs,\r
+ "Background"));\r
\r
- // MUST NOTIFY THE COLOURSCHEME OF CONSENSUS!\r
- ccs.setConsensus( viewport.vconsensus );\r
- viewport.setGlobalColourScheme(ccs);\r
+ }\r
+ else\r
+ {\r
+ cs.setConservation(null);\r
+ }\r
\r
- SliderPanel.setConservationSlider(alignPanel, ccs, "Background");\r
+ cs.setConsensus(viewport.hconsensus);\r
\r
}\r
- else\r
- {\r
- // MUST NOTIFY THE COLOURSCHEME OF CONSENSUS!\r
- if (cs != null)\r
- cs.setConsensus(viewport.vconsensus);\r
- viewport.setGlobalColourScheme(cs);\r
- }\r
-\r
+ viewport.setGlobalColourScheme(cs);\r
\r
- if(viewport.getColourAppliesToAllGroups())\r
+ if (viewport.getColourAppliesToAllGroups())\r
{\r
Vector groups = viewport.alignment.getGroups();\r
- for(int i=0; i<groups.size(); i++)\r
+ for (int i = 0; i < groups.size(); i++)\r
{\r
- SequenceGroup sg = (SequenceGroup)groups.elementAt(i);\r
+ SequenceGroup sg = (SequenceGroup) groups.elementAt(i);\r
\r
+ if(cs==null)\r
+ {\r
+ sg.cs = null;\r
+ continue;\r
+ }\r
if (cs instanceof ClustalxColourScheme)\r
{\r
- sg.cs = new ClustalxColourScheme(sg.sequences, sg.getWidth());\r
+ sg.cs = new ClustalxColourScheme(sg.getSequences(true), sg.getWidth());\r
}\r
else\r
+ {\r
try\r
{\r
sg.cs = (ColourSchemeI) cs.getClass().newInstance();\r
ex.printStackTrace();\r
sg.cs = cs;\r
}\r
+ }\r
\r
- if(viewport.getAbovePIDThreshold())\r
+ if (viewport.getAbovePIDThreshold()\r
+ || cs instanceof PIDColourScheme\r
+ || cs instanceof Blosum62ColourScheme)\r
{\r
- if (sg.cs instanceof ResidueColourScheme)\r
- ( (ResidueColourScheme) sg.cs).setThreshold(threshold);\r
- else if (sg.cs instanceof ScoreColourScheme)\r
- ( (ScoreColourScheme) sg.cs).setThreshold(threshold);\r
-\r
- sg.cs.setConsensus( AAFrequency.calculate(sg.sequences, 0, sg.getWidth()) );\r
+ sg.cs.setThreshold(threshold, viewport.getIgnoreGapsConsensus());\r
+ sg.cs.setConsensus(AAFrequency.calculate(sg.getSequences(true), 0, sg.getWidth()));\r
}\r
+ else\r
+ sg.cs.setThreshold(0, viewport.getIgnoreGapsConsensus());\r
\r
- if( viewport.getConservationSelected() )\r
+ if (viewport.getConservationSelected())\r
{\r
Conservation c = new Conservation("Group",\r
ResidueProperties.propHash, 3,\r
- sg.sequences, 0, viewport.alignment.getWidth()-1);\r
+ sg.getSequences(true), 0,\r
+ viewport.alignment.getWidth() - 1);\r
c.calculate();\r
c.verdict(false, viewport.ConsPercGaps);\r
- ConservationColourScheme ccs = new ConservationColourScheme(c, sg.cs);\r
-\r
- // MUST NOTIFY THE COLOURSCHEME OF CONSENSUS!\r
- ccs.setConsensus( AAFrequency.calculate(sg.sequences, 0, sg.getWidth()));\r
- sg.cs = ccs;\r
+ sg.cs.setConservation(c);\r
}\r
else\r
{\r
- // MUST NOTIFY THE COLOURSCHEME OF CONSENSUS!\r
- sg.cs.setConsensus(AAFrequency.calculate(sg.sequences, 0, sg.getWidth()));\r
+ sg.cs.setConservation(null);\r
+ sg.cs.setThreshold(0, viewport.getIgnoreGapsConsensus());\r
}\r
\r
}\r
}\r
\r
- if(alignPanel.getOverviewPanel()!=null)\r
+\r
+ if (alignPanel.getOverviewPanel() != null)\r
+ {\r
alignPanel.getOverviewPanel().updateOverviewImage();\r
+ }\r
\r
alignPanel.repaint();\r
}\r
\r
- protected void modifyPID_actionPerformed(ActionEvent e)\r
+\r
+\r
+ protected void modifyPID_actionPerformed()\r
{\r
- if(viewport.getAbovePIDThreshold())\r
- {\r
- SliderPanel.setPIDSliderSource(alignPanel, viewport.getGlobalColourScheme(),\r
- "Background");\r
- SliderPanel.showPIDSlider();\r
- }\r
+ if (viewport.getAbovePIDThreshold() && viewport.globalColourScheme!=null)\r
+ {\r
+ SliderPanel.setPIDSliderSource(alignPanel, viewport.getGlobalColourScheme(),\r
+ "Background");\r
+ SliderPanel.showPIDSlider();\r
+ }\r
}\r
\r
- protected void modifyConservation_actionPerformed(ActionEvent e)\r
+ protected void modifyConservation_actionPerformed()\r
{\r
- if(viewport.getConservationSelected())\r
+ if (viewport.getConservationSelected() && viewport.globalColourScheme!=null)\r
{\r
SliderPanel.setConservationSlider(alignPanel, viewport.globalColourScheme,\r
"Background");\r
}\r
}\r
\r
-\r
- protected void conservationMenuItem_actionPerformed(ActionEvent e)\r
+ protected void conservationMenuItem_actionPerformed()\r
{\r
viewport.setConservationSelected(conservationMenuItem.getState());\r
\r
viewport.setAbovePIDThreshold(false);\r
abovePIDThreshold.setState(false);\r
\r
- ColourSchemeI cs = viewport.getGlobalColourScheme();\r
- if(cs instanceof ConservationColourScheme )\r
- changeColour( ((ConservationColourScheme)cs).cs );\r
- else\r
- changeColour( cs );\r
+ changeColour(viewport.getGlobalColourScheme());\r
\r
- modifyConservation_actionPerformed(null);\r
+ modifyConservation_actionPerformed();\r
}\r
\r
- public void abovePIDThreshold_actionPerformed(ActionEvent e)\r
+ public void abovePIDThreshold_actionPerformed()\r
{\r
viewport.setAbovePIDThreshold(abovePIDThreshold.getState());\r
\r
conservationMenuItem.setState(false);\r
viewport.setConservationSelected(false);\r
\r
- ColourSchemeI cs = viewport.getGlobalColourScheme();\r
+ changeColour(viewport.getGlobalColourScheme());\r
\r
- if(cs instanceof ConservationColourScheme )\r
- changeColour( ((ConservationColourScheme)cs).cs );\r
- else\r
- changeColour( cs );\r
-\r
- modifyPID_actionPerformed(null);\r
- }\r
-\r
-\r
-\r
- public void userDefinedColour_actionPerformed(ActionEvent e)\r
- {\r
- UserDefinedColours chooser = new UserDefinedColours( alignPanel, null);\r
- }\r
-\r
- public void PIDColour_actionPerformed(ActionEvent e)\r
- {\r
- changeColour( new PIDColourScheme() );\r
- }\r
-\r
-\r
- public void BLOSUM62Colour_actionPerformed(ActionEvent e)\r
- {\r
- changeColour(new Blosum62ColourScheme() );\r
+ modifyPID_actionPerformed();\r
}\r
\r
\r
\r
- public void sortPairwiseMenuItem_actionPerformed(ActionEvent e)\r
+ public void sortPairwiseMenuItem_actionPerformed()\r
{\r
- addHistoryItem("sort");\r
- AlignmentSorter.sortByPID(viewport.getAlignment(), viewport.getAlignment().getSequenceAt(0));\r
+ SequenceI [] oldOrder = viewport.getAlignment().getSequencesArray();\r
+ AlignmentSorter.sortByPID(viewport.getAlignment(),\r
+ viewport.getAlignment().getSequenceAt(0));\r
+ addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder, viewport.alignment));\r
alignPanel.repaint();\r
}\r
\r
- public void sortIDMenuItem_actionPerformed(ActionEvent e)\r
+ public void sortIDMenuItem_actionPerformed()\r
{\r
- addHistoryItem("sort");\r
- AlignmentSorter.sortByID( viewport.getAlignment() );\r
+ // addHistoryItem(new HistoryItem("ID Sort", viewport.alignment,\r
+ // HistoryItem.SORT));\r
+ AlignmentSorter.sortByID(viewport.getAlignment());\r
alignPanel.repaint();\r
}\r
\r
- public void sortGroupMenuItem_actionPerformed(ActionEvent e)\r
+ public void sortGroupMenuItem_actionPerformed()\r
{\r
- addHistoryItem("sort");\r
+ // addHistoryItem(new HistoryItem("Group Sort", viewport.alignment,\r
+ // HistoryItem.SORT));\r
AlignmentSorter.sortByGroup(viewport.getAlignment());\r
- AlignmentSorter.sortGroups(viewport.getAlignment());\r
alignPanel.repaint();\r
+\r
}\r
\r
- public void removeRedundancyMenuItem_actionPerformed(ActionEvent e)\r
+ public void removeRedundancyMenuItem_actionPerformed()\r
{\r
- RedundancyPanel sp = new RedundancyPanel(alignPanel);\r
- Frame frame = new Frame();\r
- frame.add(sp);\r
- jalview.bin.JalviewLite.addFrame(frame, "Redundancy threshold selection", 400, 120);\r
-\r
+ new RedundancyPanel(alignPanel);\r
}\r
\r
- public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)\r
+ public void pairwiseAlignmentMenuItem_actionPerformed()\r
{\r
- if(viewport.getSelectionGroup().getSize()>1)\r
+ if (viewport.getSelectionGroup()!=null\r
+ && viewport.getSelectionGroup().getSize(false) > 1)\r
{\r
Frame frame = new Frame();\r
- frame.add(new PairwiseAlignPanel(viewport));\r
+ frame.add(new PairwiseAlignPanel(alignPanel));\r
jalview.bin.JalviewLite.addFrame(frame, "Pairwise Alignment", 600, 500);\r
}\r
}\r
\r
- public void PCAMenuItem_actionPerformed(ActionEvent e)\r
+ public void PCAMenuItem_actionPerformed()\r
{\r
+ //are the sequences aligned?\r
+ if (!viewport.alignment.isAligned())\r
+ {\r
+ SequenceI current;\r
+ int Width = viewport.getAlignment().getWidth();\r
+\r
+ for (int i = 0; i < viewport.getAlignment().getSequences().size();\r
+ i++)\r
+ {\r
+ current = viewport.getAlignment().getSequenceAt(i);\r
+\r
+ if (current.getLength() < Width)\r
+ {\r
+ current.insertCharAt(Width - 1, viewport.getGapCharacter());\r
+ }\r
+ }\r
+ alignPanel.repaint();\r
+ }\r
\r
- if( (viewport.getSelectionGroup()!=null && viewport.getSelectionGroup().getSize()<4 && viewport.getSelectionGroup().getSize()>0)\r
- || viewport.getAlignment().getHeight()<4)\r
+ if ( (viewport.getSelectionGroup() != null &&\r
+ viewport.getSelectionGroup().getSize(false) < 4 &&\r
+ viewport.getSelectionGroup().getSize(false) > 0)\r
+ || viewport.getAlignment().getHeight() < 4)\r
{\r
return;\r
}\r
\r
- try{\r
- PCAPanel pcaPanel = new PCAPanel(viewport, null);\r
- Frame frame = new Frame();\r
- frame.add(pcaPanel);\r
- jalview.bin.JalviewLite.addFrame(frame, "Principal component analysis", 400, 400);\r
- }catch(java.lang.OutOfMemoryError ex)\r
- {\r
- }\r
-\r
+ try\r
+ {\r
+ new PCAPanel(viewport);\r
+ }\r
+ catch (java.lang.OutOfMemoryError ex)\r
+ {\r
+ }\r
\r
}\r
\r
- public void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)\r
+ public void averageDistanceTreeMenuItem_actionPerformed()\r
{\r
NewTreePanel("AV", "PID", "Average distance tree using PID");\r
}\r
\r
- public void neighbourTreeMenuItem_actionPerformed(ActionEvent e)\r
+ public void neighbourTreeMenuItem_actionPerformed()\r
{\r
NewTreePanel("NJ", "PID", "Neighbour joining tree using PID");\r
}\r
\r
-\r
- protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)\r
+ protected void njTreeBlosumMenuItem_actionPerformed()\r
{\r
NewTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");\r
}\r
\r
- protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)\r
+ protected void avTreeBlosumMenuItem_actionPerformed()\r
{\r
NewTreePanel("AV", "BL", "Average distance tree using BLOSUM62PID");\r
}\r
void NewTreePanel(String type, String pwType, String title)\r
{\r
//are the sequences aligned?\r
- if(!viewport.alignment.isAligned())\r
+ if (!viewport.alignment.isAligned())\r
{\r
- return;\r
- }\r
+ SequenceI current;\r
+ int Width = viewport.getAlignment().getWidth();\r
+\r
+ for (int i = 0; i < viewport.getAlignment().getSequences().size();\r
+ i++)\r
+ {\r
+ current = viewport.getAlignment().getSequenceAt(i);\r
+\r
+ if (current.getLength() < Width)\r
+ {\r
+ current.insertCharAt(Width - 1, viewport.getGapCharacter());\r
+ }\r
+ }\r
+ alignPanel.repaint();\r
\r
- final TreePanel tp;\r
- if (viewport.getSelectionGroup() != null &&\r
- viewport.getSelectionGroup().getSize() > 3)\r
- {\r
- tp = new TreePanel(viewport, viewport.getSelectionGroup().sequences, type,\r
- pwType,\r
- 0, viewport.alignment.getWidth());\r
}\r
- else\r
+\r
+ if ( (viewport.getSelectionGroup() != null &&\r
+ viewport.getSelectionGroup().getSize(false) > 1)\r
+ || (viewport.getSelectionGroup() == null\r
+ && viewport.alignment.getHeight() > 1))\r
{\r
- tp = new TreePanel(viewport, viewport.getAlignment().getSequences(),\r
- type, pwType, 0, viewport.alignment.getWidth());\r
+ final TreePanel tp = new TreePanel(viewport,\r
+ type,\r
+ pwType);\r
+\r
+ addTreeMenuItem(tp, title);\r
+\r
+ jalview.bin.JalviewLite.addFrame(tp, title, 600, 500);\r
}\r
+ }\r
\r
- addTreeMenuItem(tp, title);\r
+ void loadTree_actionPerformed()\r
+ {\r
+ CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);\r
+ cap.setText("Paste your Newick tree file here.");\r
+ cap.treeImport = true;\r
+ Frame frame = new Frame();\r
+ frame.add(cap);\r
+ jalview.bin.JalviewLite.addFrame(frame, "Paste Newick file ", 400, 300);\r
+ }\r
\r
- jalview.bin.JalviewLite.addFrame(tp, title, 600, 500);\r
+ public void loadTree(jalview.io.NewickFile tree, String treeFile)\r
+ {\r
+ TreePanel tp = new TreePanel(viewport,\r
+ treeFile,\r
+ "From File - ",\r
+ tree);\r
+ jalview.bin.JalviewLite.addFrame(tp, treeFile, 600, 500);\r
+ addTreeMenuItem(tp, treeFile);\r
}\r
\r
void addTreeMenuItem(final TreePanel treePanel, String title)\r
sortByTreeMenu.add(item);\r
item.addActionListener(new java.awt.event.ActionListener()\r
{\r
- public void actionPerformed(ActionEvent e)\r
+ public void actionPerformed(ActionEvent evt)\r
{\r
- addHistoryItem("sort");\r
+ // addHistoryItem(new HistoryItem("Sort", viewport.alignment,\r
+ // HistoryItem.SORT));\r
AlignmentSorter.sortByTree(viewport.getAlignment(), treePanel.getTree());\r
alignPanel.repaint();\r
}\r
});\r
}\r
\r
- protected void documentation_actionPerformed(ActionEvent e) {\r
-\r
- jalview.bin.JalviewLite.showURL("http://www.jalview.org");\r
-\r
+ protected void documentation_actionPerformed()\r
+ {\r
+ showURL("http://www.jalview.org/help.html", "HELP");\r
}\r
\r
- protected void about_actionPerformed(ActionEvent e)\r
+ protected void about_actionPerformed()\r
{\r
+\r
class AboutPanel extends Canvas\r
{\r
+ String version;\r
+ public AboutPanel(String version)\r
+ { this.version = version; }\r
+\r
public void paint(Graphics g)\r
{\r
g.setColor(Color.white);\r
- g.fillRect(0,0,getSize().width, getSize().height);\r
+ g.fillRect(0, 0, getSize().width, getSize().height);\r
g.setFont(new Font("Helvetica", Font.PLAIN, 12));\r
FontMetrics fm = g.getFontMetrics();\r
int fh = fm.getHeight();\r
- int y=20, x=7;\r
+ int y = 5, x = 7;\r
g.setColor(Color.black);\r
g.setFont(new Font("Helvetica", Font.BOLD, 14));\r
- g.drawString("JalView - Release 2.0", 200,y+=fh);\r
+ g.drawString("Jalview - Release "+version, 200, y += fh);\r
g.setFont(new Font("Helvetica", Font.PLAIN, 12));\r
- g.drawString("Authors: Michele Clamp, James Cuff, Steve Searle, Andrew Waterhouse, Jim Procter & Geoff Barton.",x,y+=fh*2);\r
- g.drawString("Current development managed by Andrew Waterhouse; Barton Group, University of Dundee.",x,y+=fh);\r
- g.drawString("If you use JalView, please cite:",x,y+=fh+8);\r
- g.drawString("\"Clamp, M., Cuff, J., Searle, S. M. and Barton, G. J. (2004), The Jalview Java Alignment Editor\"",x,y+=fh);\r
- g.drawString("Bioinformatics, 2004 12;426-7.",x,y+=fh);\r
+ g.drawString("Authors: Michele Clamp, James Cuff, Steve Searle, Andrew Waterhouse, Jim Procter & Geoff Barton.",\r
+ x, y += fh * 2);\r
+ g.drawString("Current development managed by Andrew Waterhouse; Barton Group, University of Dundee.",\r
+ x, y += fh);\r
+ g.drawString(\r
+ "For any issues relating to Jalview, email help@jalview.org", x,\r
+ y += fh);\r
+ g.drawString("If you use JalView, please cite:", x, y += fh + 8);\r
+ g.drawString("\"Clamp, M., Cuff, J., Searle, S. M. and Barton, G. J. (2004), The Jalview Java Alignment Editor\"",\r
+ x, y += fh);\r
+ g.drawString("Bioinformatics, 2004 20;426-7.", x, y += fh);\r
+ }\r
+ }\r
+\r
+ String version = "test";\r
+ java.net.URL url = getClass().getResource("/.build_properties");\r
+ if (url != null)\r
+ {\r
+ try\r
+ {\r
+ BufferedReader reader = new BufferedReader(new InputStreamReader(\r
+ url.openStream()));\r
+ String line;\r
+ while ( (line = reader.readLine()) != null)\r
+ {\r
+ if (line.indexOf("VERSION") > -1)\r
+ {\r
+ version = line.substring(line.indexOf("=") + 1);\r
+ }\r
+ }\r
+ }\r
+ catch (Exception ex)\r
+ {\r
+ ex.printStackTrace();\r
}\r
}\r
+\r
+\r
Frame frame = new Frame();\r
- frame.add(new AboutPanel());\r
- jalview.bin.JalviewLite.addFrame(frame, "Jalview", 580,200);\r
+ frame.add(new AboutPanel(version));\r
+ jalview.bin.JalviewLite.addFrame(frame, "Jalview", 580, 200);\r
+\r
+ }\r
+\r
+ public void showURL(String url, String target)\r
+ {\r
+ if (viewport.applet == null)\r
+ {\r
+ System.out.println("Not running as applet - no browser available.");\r
+ }\r
+ else\r
+ {\r
+ try\r
+ {\r
+ System.out.println("Show url: "+url);\r
+ viewport.applet.getAppletContext().showDocument(new java.net.URL(url),\r
+ target);\r
+ }\r
+ catch (Exception ex)\r
+ {\r
+ ex.printStackTrace();\r
+ }\r
+ }\r
+ }\r
+\r
+\r
+ //////////////////////////////////////////////////////////////////////////////////\r
+ //JBuilder Graphics here\r
+\r
+ protected MenuBar alignFrameMenuBar = new MenuBar();\r
+ protected Menu fileMenu = new Menu("File");\r
+ protected MenuItem loadApplication = new MenuItem("View in Full Application");\r
+ protected MenuItem loadTree = new MenuItem("Load Associated Tree");\r
+ protected MenuItem closeMenuItem = new MenuItem("Close");\r
+ protected Menu editMenu = new Menu("Edit");\r
+ protected Menu viewMenu = new Menu("View");\r
+ protected Menu colourMenu = new Menu("Colour");\r
+ protected Menu calculateMenu = new Menu("Calculate");\r
+ protected MenuItem selectAllSequenceMenuItem = new MenuItem("Select all");\r
+ protected MenuItem deselectAllSequenceMenuItem = new MenuItem("Deselect All");\r
+ protected MenuItem invertSequenceMenuItem = new MenuItem("Invert Selection");\r
+ protected MenuItem remove2LeftMenuItem = new MenuItem();\r
+ protected MenuItem remove2RightMenuItem = new MenuItem();\r
+ protected MenuItem removeGappedColumnMenuItem = new MenuItem();\r
+ protected MenuItem removeAllGapsMenuItem = new MenuItem();\r
+ protected CheckboxMenuItem viewBoxesMenuItem = new CheckboxMenuItem();\r
+ protected CheckboxMenuItem viewTextMenuItem = new CheckboxMenuItem();\r
+ protected MenuItem sortPairwiseMenuItem = new MenuItem();\r
+ protected MenuItem sortIDMenuItem = new MenuItem();\r
+ protected MenuItem sortGroupMenuItem = new MenuItem();\r
+ protected MenuItem removeRedundancyMenuItem = new MenuItem();\r
+ protected MenuItem pairwiseAlignmentMenuItem = new MenuItem();\r
+ protected MenuItem PCAMenuItem = new MenuItem();\r
+ protected MenuItem averageDistanceTreeMenuItem = new MenuItem();\r
+ protected MenuItem neighbourTreeMenuItem = new MenuItem();\r
+ BorderLayout borderLayout1 = new BorderLayout();\r
+ public Label statusBar = new Label();\r
+ protected Menu outputTextboxMenu = new Menu();\r
+ protected MenuItem clustalColour = new MenuItem();\r
+ protected MenuItem zappoColour = new MenuItem();\r
+ protected MenuItem taylorColour = new MenuItem();\r
+ protected MenuItem hydrophobicityColour = new MenuItem();\r
+ protected MenuItem helixColour = new MenuItem();\r
+ protected MenuItem strandColour = new MenuItem();\r
+ protected MenuItem turnColour = new MenuItem();\r
+ protected MenuItem buriedColour = new MenuItem();\r
+ protected MenuItem userDefinedColour = new MenuItem();\r
+ protected MenuItem PIDColour = new MenuItem();\r
+ protected MenuItem BLOSUM62Colour = new MenuItem();\r
+ MenuItem njTreeBlosumMenuItem = new MenuItem();\r
+ MenuItem avDistanceTreeBlosumMenuItem = new MenuItem();\r
+ protected CheckboxMenuItem annotationPanelMenuItem = new CheckboxMenuItem();\r
+ protected CheckboxMenuItem colourTextMenuItem = new CheckboxMenuItem();\r
+ MenuItem overviewMenuItem = new MenuItem();\r
+ protected MenuItem undoMenuItem = new MenuItem();\r
+ protected MenuItem redoMenuItem = new MenuItem();\r
+ protected CheckboxMenuItem conservationMenuItem = new CheckboxMenuItem();\r
+ MenuItem noColourmenuItem = new MenuItem();\r
+ protected CheckboxMenuItem wrapMenuItem = new CheckboxMenuItem();\r
+ protected CheckboxMenuItem renderGapsMenuItem = new CheckboxMenuItem();\r
+ MenuItem findMenuItem = new MenuItem();\r
+ protected CheckboxMenuItem abovePIDThreshold = new CheckboxMenuItem();\r
+ protected MenuItem nucleotideColour = new MenuItem();\r
+ MenuItem deleteGroups = new MenuItem();\r
+ MenuItem delete = new MenuItem();\r
+ MenuItem copy = new MenuItem();\r
+ MenuItem cut = new MenuItem();\r
+ Menu pasteMenu = new Menu();\r
+ MenuItem pasteNew = new MenuItem();\r
+ MenuItem pasteThis = new MenuItem();\r
+ protected CheckboxMenuItem applyToAllGroups = new CheckboxMenuItem();\r
+ protected MenuItem font = new MenuItem();\r
+ protected CheckboxMenuItem scaleAbove = new CheckboxMenuItem();\r
+ protected CheckboxMenuItem scaleLeft = new CheckboxMenuItem();\r
+ protected CheckboxMenuItem scaleRight = new CheckboxMenuItem();\r
+ MenuItem modifyPID = new MenuItem();\r
+ MenuItem modifyConservation = new MenuItem();\r
+ protected CheckboxMenuItem autoCalculate\r
+ = new CheckboxMenuItem("Autocalculate Consensus", true);\r
+ protected Menu sortByTreeMenu = new Menu();\r
+ Menu sort = new Menu();\r
+ Menu calculate = new Menu();\r
+ MenuItem inputText = new MenuItem();\r
+ Menu helpMenu = new Menu();\r
+ MenuItem documentation = new MenuItem();\r
+ MenuItem about = new MenuItem();\r
+ protected CheckboxMenuItem seqLimits = new CheckboxMenuItem();\r
+ Panel embeddedMenu;\r
+ Label embeddedEdit;\r
+ Label embeddedSelect;\r
+ Label embeddedView;\r
+ Label embeddedFormat;\r
+ Label embeddedColour;\r
+ Label embeddedFile;\r
+ Label embeddedHelp;\r
+ Label embeddedCalculate;\r
+ FlowLayout flowLayout1;\r
+\r
+ private void jbInit() throws Exception {\r
+\r
+ setMenuBar(alignFrameMenuBar);\r
+\r
+ MenuItem item;\r
+\r
+ // dynamically fill save as menu with available formats\r
+ for (int i = 0; i < jalview.io.AppletFormatAdapter.WRITEABLE_FORMATS.length; i++)\r
+ {\r
+\r
+ item = new MenuItem( jalview.io.AppletFormatAdapter.WRITEABLE_FORMATS[i]);\r
+\r
+ item.addActionListener(new java.awt.event.ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent e)\r
+ {\r
+ outputText_actionPerformed(e);\r
+ }\r
+ });\r
+\r
+ outputTextboxMenu.add(item);\r
+ }\r
+ closeMenuItem.addActionListener(this);\r
+ loadApplication.addActionListener(this);\r
+\r
+ loadTree.addActionListener(this);\r
+ selectAllSequenceMenuItem.addActionListener(this);\r
+ deselectAllSequenceMenuItem.addActionListener(this);\r
+ invertSequenceMenuItem.addActionListener(this);\r
+ remove2LeftMenuItem.setLabel("Remove Left");\r
+ remove2LeftMenuItem.addActionListener(this);\r
+ remove2RightMenuItem.setLabel("Remove Right");\r
+ remove2RightMenuItem.addActionListener(this);\r
+ removeGappedColumnMenuItem.setLabel("Remove Empty Columns");\r
+ removeGappedColumnMenuItem.addActionListener(this);\r
+ removeAllGapsMenuItem.setLabel("Remove All Gaps");\r
+ removeAllGapsMenuItem.addActionListener(this);\r
+ viewBoxesMenuItem.setLabel("Boxes");\r
+ viewBoxesMenuItem.setState(true);\r
+ viewBoxesMenuItem.addItemListener(this);\r
+ viewTextMenuItem.setLabel("Text");\r
+ viewTextMenuItem.setState(true);\r
+ viewTextMenuItem.addItemListener(this);\r
+ sortPairwiseMenuItem.setLabel("by Pairwise Identity");\r
+ sortPairwiseMenuItem.addActionListener(this);\r
+ sortIDMenuItem.setLabel("by ID");\r
+ sortIDMenuItem.addActionListener(this);\r
+ sortGroupMenuItem.setLabel("by Group");\r
+ sortGroupMenuItem.addActionListener(this);\r
+ removeRedundancyMenuItem.setLabel("Remove Redundancy...");\r
+ removeRedundancyMenuItem.addActionListener(this);\r
+ pairwiseAlignmentMenuItem.setLabel("Pairwise Alignments...");\r
+ pairwiseAlignmentMenuItem.addActionListener(this);\r
+ PCAMenuItem.setLabel("Principal Component Analysis");\r
+ PCAMenuItem.addActionListener(this);\r
+ averageDistanceTreeMenuItem.setLabel(\r
+ "Average Distance Using % Identity");\r
+ averageDistanceTreeMenuItem.addActionListener(this);\r
+ neighbourTreeMenuItem.setLabel("Neighbour Joining Using % Identity");\r
+ neighbourTreeMenuItem.addActionListener(this);\r
+ alignFrameMenuBar.setFont(new java.awt.Font("Verdana", 0, 11));\r
+ statusBar.setBackground(Color.white);\r
+ statusBar.setFont(new java.awt.Font("Verdana", 0, 11));\r
+ statusBar.setText("Status bar");\r
+ outputTextboxMenu.setLabel("Output to Textbox");\r
+ clustalColour.setLabel("Clustalx");\r
+\r
+ clustalColour.addActionListener(this);\r
+ zappoColour.setLabel("Zappo");\r
+ zappoColour.addActionListener(this);\r
+ taylorColour.setLabel("Taylor");\r
+ taylorColour.addActionListener(this);\r
+ hydrophobicityColour.setLabel("Hydrophobicity");\r
+ hydrophobicityColour.addActionListener(this);\r
+ helixColour.setLabel("Helix Propensity");\r
+ helixColour.addActionListener(this);\r
+ strandColour.setLabel("Strand Propensity");\r
+ strandColour.addActionListener(this);\r
+ turnColour.setLabel("Turn Propensity");\r
+ turnColour.addActionListener(this);\r
+ buriedColour.setLabel("Buried Index");\r
+ buriedColour.addActionListener(this);\r
+ userDefinedColour.setLabel("User Defined...");\r
+ userDefinedColour.addActionListener(this);\r
+ PIDColour.setLabel("Percentage Identity");\r
+ PIDColour.addActionListener(this);\r
+ BLOSUM62Colour.setLabel("BLOSUM62 Score");\r
+ BLOSUM62Colour.addActionListener(this);\r
+ avDistanceTreeBlosumMenuItem.setLabel(\r
+ "Average Distance Using BLOSUM62");\r
+ avDistanceTreeBlosumMenuItem.addActionListener(this);\r
+ njTreeBlosumMenuItem.setLabel("Neighbour Joining Using BLOSUM62");\r
+ njTreeBlosumMenuItem.addActionListener(this);\r
+ annotationPanelMenuItem.setLabel("Show Annotations");\r
+ annotationPanelMenuItem.addItemListener(this);\r
+ colourTextMenuItem.setLabel("Colour Text");\r
+ colourTextMenuItem.addItemListener(this);\r
+ overviewMenuItem.setLabel("Overview Window");\r
+ overviewMenuItem.addActionListener(this);\r
+ undoMenuItem.setEnabled(false);\r
+ undoMenuItem.setLabel("Undo");\r
+ undoMenuItem.addActionListener(this);\r
+ redoMenuItem.setEnabled(false);\r
+ redoMenuItem.setLabel("Redo");\r
+ redoMenuItem.addActionListener(this);\r
+ conservationMenuItem.setLabel("by Conservation");\r
+ conservationMenuItem.addItemListener(this);\r
+ noColourmenuItem.setLabel("None");\r
+ noColourmenuItem.addActionListener(this);\r
+ wrapMenuItem.setLabel("Wrap");\r
+ wrapMenuItem.addItemListener(this);\r
+ renderGapsMenuItem.setLabel("Show Gaps");\r
+ renderGapsMenuItem.setState(true);\r
+ renderGapsMenuItem.addItemListener(this);\r
+ findMenuItem.setLabel("Find...");\r
+ findMenuItem.addActionListener(this);\r
+ abovePIDThreshold.setLabel("Above Identity Threshold");\r
+ abovePIDThreshold.addItemListener(this);\r
+ nucleotideColour.setLabel("Nucleotide");\r
+ nucleotideColour.addActionListener(this);\r
+ deleteGroups.setLabel("Undefine Groups");\r
+ deleteGroups.addActionListener(this);\r
+ copy.setLabel("Copy");\r
+ copy.addActionListener(this);\r
+ cut.setLabel("Cut");\r
+ cut.addActionListener(this);\r
+ delete.setLabel("Delete");\r
+ delete.addActionListener(this);\r
+ pasteMenu.setLabel("Paste");\r
+ pasteNew.setLabel("To New Alignment");\r
+ pasteNew.addActionListener(this);\r
+ pasteThis.setLabel("Add To This Alignment");\r
+ pasteThis.addActionListener(this);\r
+ applyToAllGroups.setLabel("Apply Colour To All Groups");\r
+ applyToAllGroups.setState(true);\r
+ applyToAllGroups.addItemListener(this);\r
+ font.setLabel("Font...");\r
+ font.addActionListener(this);\r
+ scaleAbove.setLabel("Scale Above");\r
+ scaleAbove.setState(true);\r
+ scaleAbove.setEnabled(false);\r
+ scaleAbove.addItemListener(this);\r
+ scaleLeft.setEnabled(false);\r
+ scaleLeft.setState(true);\r
+ scaleLeft.setLabel("Scale Left");\r
+ scaleLeft.addItemListener(this);\r
+ scaleRight.setEnabled(false);\r
+ scaleRight.setState(true);\r
+ scaleRight.setLabel("Scale Right");\r
+ scaleRight.addItemListener(this);\r
+ modifyPID.setLabel("Modify Identity Threshold...");\r
+ modifyPID.addActionListener(this);\r
+ modifyConservation.setLabel("Modify Conservation Threshold...");\r
+ modifyConservation.addActionListener(this);\r
+ sortByTreeMenu.setLabel("By Tree Order");\r
+ sort.setLabel("Sort");\r
+ calculate.setLabel("Calculate Tree");\r
+ autoCalculate.addItemListener(this);\r
+ inputText.setLabel("Input from textbox");\r
+ inputText.addActionListener(this);\r
+\r
+ helpMenu.setLabel("Help");\r
+ documentation.setLabel("Documentation");\r
+ documentation.addActionListener(this);\r
+\r
+ about.setLabel("About...");\r
+ about.addActionListener(this);\r
+ seqLimits.setState(true);\r
+ seqLimits.setLabel("Show Sequence Limits");\r
+ seqLimits.addItemListener(this);\r
+ featureSettings.setLabel("Feature Settings...");\r
+ featureSettings.addActionListener(this);\r
+ sequenceFeatures.setLabel("Sequence Features");\r
+ sequenceFeatures.addItemListener(this);\r
+ sequenceFeatures.setState(false);\r
+ annotationColour.setLabel("by Annotation...");\r
+ annotationColour.addActionListener(this);\r
+ invertSequenceMenuItem.setLabel("Invert Sequence Selection");\r
+ invertColSel.setLabel("Invert Column Selection");\r
+ menu1.setLabel("Show");\r
+ showColumns.setLabel("All Columns ");\r
+ showSeqs.setLabel("All Sequences");\r
+ menu2.setLabel("Hide");\r
+ hideColumns.setLabel("Selected Columns");\r
+ hideSequences.setLabel("Selected Sequences");\r
+ invertColSel.addActionListener(this);\r
+ showColumns.addActionListener(this);\r
+ showSeqs.addActionListener(this);\r
+ hideColumns.addActionListener(this);\r
+ hideSequences.addActionListener(this);\r
+ formatMenu.setLabel("Format");\r
+ selectMenu.setLabel("Select");\r
+ newView.setLabel("New View");\r
+ newView.addActionListener(this);\r
+ alignFrameMenuBar.add(fileMenu);\r
+ alignFrameMenuBar.add(editMenu);\r
+ alignFrameMenuBar.add(selectMenu);\r
+ alignFrameMenuBar.add(viewMenu);\r
+ alignFrameMenuBar.add(formatMenu);\r
+ alignFrameMenuBar.add(colourMenu);\r
+ alignFrameMenuBar.add(calculateMenu);\r
+ alignFrameMenuBar.add(helpMenu);\r
+ fileMenu.add(inputText);\r
+ fileMenu.add(outputTextboxMenu);\r
+ if(jalviewServletURL!=null)\r
+ fileMenu.add(loadApplication);\r
+ fileMenu.addSeparator();\r
+ fileMenu.add(loadTree);\r
+ fileMenu.add(closeMenuItem);\r
+ editMenu.add(undoMenuItem);\r
+ editMenu.add(redoMenuItem);\r
+ editMenu.add(cut);\r
+ editMenu.add(copy);\r
+ editMenu.add(pasteMenu);\r
+ editMenu.add(delete);\r
+ editMenu.addSeparator();\r
+ editMenu.add(remove2LeftMenuItem);\r
+ editMenu.add(remove2RightMenuItem);\r
+ editMenu.add(removeGappedColumnMenuItem);\r
+ editMenu.add(removeAllGapsMenuItem);\r
+ editMenu.add(removeRedundancyMenuItem);\r
+ viewMenu.add(newView);\r
+ viewMenu.addSeparator();\r
+ viewMenu.add(menu1);\r
+ viewMenu.add(menu2);\r
+ viewMenu.addSeparator();\r
+ viewMenu.add(annotationPanelMenuItem);\r
+ viewMenu.addSeparator();\r
+ viewMenu.add(sequenceFeatures);\r
+ viewMenu.add(featureSettings);\r
+ viewMenu.addSeparator();\r
+ viewMenu.add(overviewMenuItem);\r
+ colourMenu.add(applyToAllGroups);\r
+ colourMenu.addSeparator();\r
+ colourMenu.add(noColourmenuItem);\r
+ colourMenu.add(clustalColour);\r
+ colourMenu.add(BLOSUM62Colour);\r
+ colourMenu.add(PIDColour);\r
+ colourMenu.add(zappoColour);\r
+ colourMenu.add(taylorColour);\r
+ colourMenu.add(hydrophobicityColour);\r
+ colourMenu.add(helixColour);\r
+ colourMenu.add(strandColour);\r
+ colourMenu.add(turnColour);\r
+ colourMenu.add(buriedColour);\r
+ colourMenu.add(nucleotideColour);\r
+ colourMenu.add(userDefinedColour);\r
+ colourMenu.addSeparator();\r
+ colourMenu.add(conservationMenuItem);\r
+ colourMenu.add(modifyConservation);\r
+ colourMenu.add(abovePIDThreshold);\r
+ colourMenu.add(modifyPID);\r
+ colourMenu.add(annotationColour);\r
+ calculateMenu.add(sort);\r
+ calculateMenu.add(calculate);\r
+ calculateMenu.addSeparator();\r
+ calculateMenu.add(pairwiseAlignmentMenuItem);\r
+ calculateMenu.add(PCAMenuItem);\r
+ calculateMenu.add(autoCalculate);\r
+ this.add(statusBar, BorderLayout.SOUTH);\r
+ pasteMenu.add(pasteNew);\r
+ pasteMenu.add(pasteThis);\r
+ sort.add(sortIDMenuItem);\r
+ sort.add(sortByTreeMenu);\r
+ sort.add(sortGroupMenuItem);\r
+ sort.add(sortPairwiseMenuItem);\r
+ calculate.add(averageDistanceTreeMenuItem);\r
+ calculate.add(neighbourTreeMenuItem);\r
+ calculate.add(avDistanceTreeBlosumMenuItem);\r
+ calculate.add(njTreeBlosumMenuItem);\r
+ helpMenu.add(documentation);\r
+ helpMenu.add(about);\r
+ menu1.add(showColumns);\r
+ menu1.add(showSeqs);\r
+ menu2.add(hideColumns);\r
+ menu2.add(hideSequences);\r
+ formatMenu.add(font);\r
+ formatMenu.add(seqLimits);\r
+ formatMenu.add(wrapMenuItem);\r
+ formatMenu.add(scaleAbove);\r
+ formatMenu.add(scaleLeft);\r
+ formatMenu.add(scaleRight);\r
+ formatMenu.add(viewBoxesMenuItem);\r
+ formatMenu.add(viewTextMenuItem);\r
+ formatMenu.add(colourTextMenuItem);\r
+ formatMenu.add(renderGapsMenuItem);\r
+ selectMenu.add(findMenuItem);\r
+ selectMenu.addSeparator();\r
+ selectMenu.add(selectAllSequenceMenuItem);\r
+ selectMenu.add(deselectAllSequenceMenuItem);\r
+ selectMenu.add(invertSequenceMenuItem);\r
+ selectMenu.add(invertColSel);\r
+ selectMenu.add(deleteGroups);\r
+ }\r
+\r
+ public void setEmbedded()\r
+ {\r
+\r
+ embeddedMenu = new Panel();\r
+ embeddedEdit = new Label("Edit");\r
+ embeddedSelect = new Label("Select");\r
+ embeddedView = new Label("View");\r
+ embeddedFormat = new Label("Format");\r
+ embeddedColour = new Label("Colour");\r
+ embeddedFile = new Label("File");\r
+ embeddedHelp = new Label("Help");\r
+ embeddedCalculate = new Label("Calculate");\r
+ flowLayout1 = new FlowLayout();\r
+ embeddedMenu.setBackground(Color.lightGray);\r
+ embeddedMenu.setLayout(flowLayout1);\r
+ embeddedEdit.setFont(new java.awt.Font("Arial", Font.PLAIN, 10));\r
+ embeddedSelect.setFont(new java.awt.Font("Arial", Font.PLAIN, 10));\r
+ embeddedView.setFont(new java.awt.Font("Arial", Font.PLAIN, 10));\r
+ embeddedFormat.setFont(new java.awt.Font("Arial", Font.PLAIN, 10));\r
+ embeddedColour.setFont(new java.awt.Font("Arial", Font.PLAIN, 10));\r
+ embeddedFile.setFont(new java.awt.Font("Arial", Font.PLAIN, 10));\r
+ embeddedHelp.setFont(new java.awt.Font("Arial", Font.PLAIN, 10));\r
+ embeddedCalculate.setFont(new java.awt.Font("Arial", Font.PLAIN, 10));\r
+ embeddedMenu.add(embeddedFile);\r
+ embeddedMenu.add(embeddedEdit);\r
+ embeddedMenu.add(embeddedSelect);\r
+ embeddedMenu.add(embeddedView);\r
+ embeddedMenu.add(embeddedFormat);\r
+ embeddedMenu.add(embeddedColour);\r
+ embeddedMenu.add(embeddedCalculate);\r
+ embeddedMenu.add(embeddedHelp);\r
+ flowLayout1.setAlignment(FlowLayout.LEFT);\r
+ flowLayout1.setHgap(2);\r
+ flowLayout1.setVgap(0);\r
+ embeddedFile.addMouseListener(this);\r
+ embeddedEdit.addMouseListener(this);\r
+ embeddedSelect.addMouseListener(this);\r
+ embeddedView.addMouseListener(this);\r
+ embeddedFormat.addMouseListener(this);\r
+ embeddedColour.addMouseListener(this);\r
+ embeddedCalculate.addMouseListener(this);\r
+ embeddedHelp.addMouseListener(this);\r
+\r
+ // setVisible(false);\r
+ fileMenu.remove(closeMenuItem);\r
+ fileMenu.remove(3); // Seperator\r
+\r
+ viewport.applet.setLayout(new BorderLayout());\r
+ viewport.applet.add(embeddedMenu, BorderLayout.NORTH);\r
+ viewport.applet.add(statusBar, BorderLayout.SOUTH);\r
+ // viewport.applet.validate();\r
+\r
+ alignPanel.setSize(viewport.applet.size().width, viewport.applet.size().height\r
+ - embeddedMenu.HEIGHT - statusBar.HEIGHT);\r
+\r
+ viewport.applet.add(alignPanel, BorderLayout.CENTER);\r
+ viewport.applet.validate();\r
+\r
+ }\r
+\r
+\r
+\r
+ PopupMenu filePopup, editPopup, searchPopup,\r
+ viewPopup, formatPopup, colourPopup, calculatePopup, helpPopup;\r
+ MenuItem featureSettings = new MenuItem();\r
+ CheckboxMenuItem sequenceFeatures = new CheckboxMenuItem();\r
+ MenuItem annotationColour = new MenuItem();\r
+ MenuItem invertColSel = new MenuItem();\r
+ Menu menu1 = new Menu();\r
+ MenuItem showColumns = new MenuItem();\r
+ MenuItem showSeqs = new MenuItem();\r
+ Menu menu2 = new Menu();\r
+ MenuItem hideColumns = new MenuItem();\r
+ MenuItem hideSequences = new MenuItem();\r
+ Menu formatMenu = new Menu();\r
+ Menu selectMenu = new Menu();\r
+ MenuItem newView = new MenuItem();\r
+\r
+ public void mousePressed(MouseEvent evt)\r
+ {\r
+ PopupMenu popup = null;\r
+ Label source = (Label)evt.getSource();\r
+ if(source==embeddedFile)\r
+ {\r
+ popup = filePopup = genPopupMenu(filePopup, fileMenu);\r
+ }\r
+ else if(source==embeddedEdit)\r
+ {\r
+ popup = editPopup = genPopupMenu(editPopup, editMenu);\r
+ }\r
+ else if(source==embeddedSelect)\r
+ {\r
+ popup = searchPopup = genPopupMenu(searchPopup, selectMenu);\r
+ }\r
+ else if(source==embeddedView)\r
+ {\r
+ popup = viewPopup = genPopupMenu(viewPopup, viewMenu);\r
+ }\r
+ else if (source ==embeddedFormat)\r
+ {\r
+ popup = formatPopup = genPopupMenu(formatPopup, formatMenu);\r
+ }\r
+ else if(source==embeddedColour)\r
+ {\r
+ popup = colourPopup = genPopupMenu(colourPopup, colourMenu);\r
+ }\r
+ else if(source==embeddedCalculate)\r
+ {\r
+ popup = calculatePopup = genPopupMenu(calculatePopup, calculateMenu);\r
+ }\r
+ else if(source==embeddedHelp)\r
+ {\r
+ popup = helpPopup = genPopupMenu(helpPopup, helpMenu);\r
+ }\r
\r
+ embeddedMenu.add(popup);\r
+ popup.show(embeddedMenu,\r
+ source.getBounds().x,\r
+ source.getBounds().y + source.getBounds().getSize().height);\r
+ }\r
\r
+ PopupMenu genPopupMenu(PopupMenu popup, Menu original)\r
+ {\r
+ if(popup!=null)\r
+ {\r
+ return popup;\r
+ }\r
+ popup = new PopupMenu();\r
+ int m, mSize = original.getItemCount();\r
+ for(m=0; m<mSize; m++)\r
+ {\r
+ popup.add(original.getItem(m));\r
+ mSize--;\r
+ m--;\r
+ }\r
\r
+ return popup;\r
}\r
+ public void mouseClicked(MouseEvent evt)\r
+ {}\r
+ public void mouseReleased(MouseEvent evt)\r
+ {}\r
+ public void mouseEntered(MouseEvent evt)\r
+ {}\r
+ public void mouseExited(MouseEvent evt)\r
+ {}\r
+\r
}\r
+\r