X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FAlignFrame.java;h=de19fd8bfdf9f428e8ca5ae5d41befea3dd2ff23;hb=6d58edc047af16d3d632842be665ff990de74607;hp=25b74b6718163d0cf596f383ddb19b68ebf6211d;hpb=4ebc6d5b362bc093c39312aa1a69836e3dd6ae84;p=jalview.git diff --git a/src/jalview/appletgui/AlignFrame.java b/src/jalview/appletgui/AlignFrame.java index 25b74b6..de19fd8 100755 --- a/src/jalview/appletgui/AlignFrame.java +++ b/src/jalview/appletgui/AlignFrame.java @@ -1,6 +1,6 @@ /* * Jalview - A Sequence Alignment Editor and Viewer - * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License @@ -19,72 +19,621 @@ package jalview.appletgui; -import jalview.jbappletgui.GAlignFrame; import jalview.schemes.*; import jalview.datamodel.*; import jalview.analysis.*; import jalview.io.*; +import jalview.commands.*; import java.awt.*; import java.awt.event.*; import java.util.*; +import java.io.InputStreamReader; +import java.io.BufferedReader; +import java.net.URL; -public class AlignFrame - extends GAlignFrame + +public class AlignFrame extends Frame implements ActionListener, + ItemListener, KeyListener, MouseListener { - final AlignmentPanel alignPanel; - final AlignViewport viewport; - public static final int NEW_WINDOW_WIDTH = 700; - public static final int NEW_WINDOW_HEIGHT = 500; - jalview.bin.JalviewLite applet; + public AlignmentPanel alignPanel; + public AlignViewport viewport; + int DEFAULT_WIDTH = 700; + int DEFAULT_HEIGHT = 500; + + String jalviewServletURL; - public AlignFrame(AlignmentI al) - { - this.applet = null; - viewport = new AlignViewport(al, null); - alignPanel = new AlignmentPanel(this, viewport); - add(alignPanel); - alignPanel.validate(); - } - public AlignFrame(AlignmentI al, jalview.bin.JalviewLite applet) + public AlignFrame(AlignmentI al, + jalview.bin.JalviewLite applet, + String title, + boolean embedded) { - this.applet = applet; + + jalviewServletURL = applet.getParameter("APPLICATION_URL"); + + try{ + jbInit(); + }catch(Exception ex) + { + ex.printStackTrace(); + } + viewport = new AlignViewport(al, applet); alignPanel = new AlignmentPanel(this, viewport); - add(alignPanel); - alignPanel.validate(); - String treeFile = applet.getParameter("treeFile"); - TreePanel treepanel = null; - if (treeFile != null) + viewport.updateConservation(alignPanel); + viewport.updateConsensus(alignPanel); + + annotationPanelMenuItem.setState(viewport.showAnnotation); + + seqLimits.setState(viewport.showJVSuffix); + + if(applet!=null) { - try + String param = applet.getParameter("sortBy"); + if (param != null) { - treeFile = treeFile; - jalview.io.NewickFile fin = new jalview.io.NewickFile(applet. - getCodeBase() + treeFile, "URL"); - fin.parse(); + if (param.equalsIgnoreCase("Id")) + sortIDMenuItem_actionPerformed(); + else if (param.equalsIgnoreCase("Pairwise Identity")) + sortPairwiseMenuItem_actionPerformed(); + } - if (fin.getTree() != null) + param = applet.getParameter("wrap"); + if (param != null) + { + if (param.equalsIgnoreCase("true")) { - TreePanel tp = null; - tp = new TreePanel(viewport, viewport.getAlignment().getSequences(), - fin, "FromFile", applet.getCodeBase() + treeFile); - jalview.bin.JalviewLite.addFrame(tp, treeFile, 600, 500); - addTreeMenuItem(tp, treeFile); + wrapMenuItem.setState(true); + wrapMenuItem_actionPerformed(); } } - catch (Exception ex) + + try { - ex.printStackTrace(); + param = applet.getParameter("windowWidth"); + if (param != null) + { + int width = Integer.parseInt(param); + DEFAULT_WIDTH = width; + } + param = applet.getParameter("windowHeight"); + if (param != null) + { + int height = Integer.parseInt(param); + DEFAULT_HEIGHT = height; + } } + catch (Exception ex) + {} + } + //Some JVMS send keyevents to Top frame or lowest panel, + //Havent worked out why yet. So add to both this frame and seqCanvas for now + this.addKeyListener(this); + alignPanel.seqPanel.seqCanvas.addKeyListener(this); + alignPanel.idPanel.idCanvas.addKeyListener(this); + alignPanel.scalePanel.addKeyListener(this); + alignPanel.annotationPanel.addKeyListener(this); + + + if(embedded) + { + setEmbedded(); + } + else + { + add(alignPanel, BorderLayout.CENTER); + jalview.bin.JalviewLite.addFrame(this, title, DEFAULT_WIDTH, + DEFAULT_HEIGHT); + } + alignPanel.validate(); + alignPanel.repaint(); + } + public AlignViewport getAlignViewport() + { + return viewport; } - public void inputText_actionPerformed(ActionEvent e) + public SeqCanvas getSeqcanvas() { - CutAndPasteTransfer cap = new CutAndPasteTransfer(true); + return alignPanel.seqPanel.seqCanvas; + } + + + /** + * DOCUMENT ME! + * + * @param String DOCUMENT ME! + */ + + public void parseFeaturesFile(String file, String type) + { + Hashtable featureLinks = new Hashtable(); + boolean featuresFile = false; + try{ + featuresFile = new jalview.io.FeaturesFile(file, type).parse(viewport.alignment, + alignPanel.seqPanel.seqCanvas. + getFeatureRenderer().featureColours, + featureLinks, + true); + } + catch(Exception ex) + { + ex.printStackTrace(); + } + + if(featuresFile) + { + if(featureLinks.size()>0) + alignPanel.seqPanel.seqCanvas + .getFeatureRenderer().featureLinks = featureLinks; + viewport.showSequenceFeatures = true; + sequenceFeatures.setState(true); + alignPanel.repaint(); + } + + } + + + public void keyPressed(KeyEvent evt) + { + if (viewport.cursorMode + && evt.getKeyCode() >= KeyEvent.VK_0 + && evt.getKeyCode() <= KeyEvent.VK_9) + { + alignPanel.seqPanel.numberPressed(evt.getKeyChar()); + } + + switch (evt.getKeyCode()) + { + case 27: // escape key + deselectAllSequenceMenuItem_actionPerformed(); + break; + case KeyEvent.VK_X: + if (evt.isControlDown() || evt.isMetaDown()) + { + cut_actionPerformed(); + } + break; + case KeyEvent.VK_C: + if (viewport.cursorMode && !evt.isControlDown()) + { + alignPanel.seqPanel.setCursorColumn(); + } + if (evt.isControlDown() || evt.isMetaDown()) + { + copy_actionPerformed(); + } + break; + case KeyEvent.VK_V: + if (evt.isControlDown()) + { + paste(evt.isShiftDown()); + } + break; + case KeyEvent.VK_A: + if (evt.isControlDown() || evt.isMetaDown()) + { + selectAllSequenceMenuItem_actionPerformed(); + } + break; + case KeyEvent.VK_DOWN: + if(viewport.cursorMode) + { + alignPanel.seqPanel.moveCursor(0,1); + } + else + moveSelectedSequences(false); + break; + + case KeyEvent.VK_UP: + if (viewport.cursorMode) + { + alignPanel.seqPanel.moveCursor(0,-1); + } + else + moveSelectedSequences(true); + break; + + case KeyEvent.VK_LEFT: + if(viewport.cursorMode) + { + alignPanel.seqPanel.moveCursor(-1,0); + } + break; + + case KeyEvent.VK_RIGHT: + if (viewport.cursorMode) + { + alignPanel.seqPanel.moveCursor(1,0); + } + break; + case KeyEvent.VK_SPACE: + if(viewport.cursorMode) + { + alignPanel.seqPanel.insertGapAtCursor(evt.isControlDown() + || evt.isShiftDown() + || evt.isAltDown() + ); + } + break; + + case KeyEvent.VK_DELETE: + case KeyEvent.VK_BACK_SPACE: + if(viewport.cursorMode) + { + alignPanel.seqPanel.deleteGapAtCursor(evt.isControlDown() + || evt.isShiftDown() + || evt.isAltDown()); + } + else + { + cut_actionPerformed(); + alignPanel.seqPanel.seqCanvas.repaint(); + } + break; + + case KeyEvent.VK_S: + if(viewport.cursorMode) + { + alignPanel.seqPanel.setCursorRow(); + } + break; + case KeyEvent.VK_P: + if(viewport.cursorMode) + { + alignPanel.seqPanel.setCursorPosition(); + } + break; + + case KeyEvent.VK_ENTER: + case KeyEvent.VK_COMMA: + if(viewport.cursorMode) + { + alignPanel.seqPanel.setCursorRowAndColumn(); + } + break; + + case KeyEvent.VK_Q: + if(viewport.cursorMode) + { + alignPanel.seqPanel.setSelectionAreaAtCursor(true); + } + break; + case KeyEvent.VK_M: + if(viewport.cursorMode) + { + alignPanel.seqPanel.setSelectionAreaAtCursor(false); + } + break; + + case KeyEvent.VK_F2: + viewport.cursorMode = ! viewport.cursorMode; + statusBar.setText("Keyboard editing mode is "+ + (viewport.cursorMode ? "on" : "off")); + if(viewport.cursorMode) + { + alignPanel.seqPanel.seqCanvas.cursorX = viewport.startRes; + alignPanel.seqPanel.seqCanvas.cursorY = viewport.startSeq; + } + break; + + case KeyEvent.VK_F: + if (evt.isControlDown()) + { + findMenuItem_actionPerformed(); + } + break; + + case KeyEvent.VK_H: + { + boolean toggleSeqs = !evt.isControlDown(); + boolean toggleCols = !evt.isShiftDown(); + boolean hide = false; + SequenceGroup sg = viewport.getSelectionGroup(); + + if(toggleSeqs) + { + if (sg != null && sg.getSize(false) != viewport.alignment.getHeight()) + { + hide = true; + viewport.hideAllSelectedSeqs(); + } + else if (!(toggleCols && viewport.colSel.getSelected().size() > 0)) + viewport.showAllHiddenSeqs(); + } + + if(toggleCols) + { + if (viewport.colSel.getSelected().size() > 0) + { + viewport.hideSelectedColumns(); + if(!toggleSeqs) + viewport.selectionGroup = sg; + } + else if (!hide) + viewport.showAllHiddenColumns(); + } + break; + } + + case KeyEvent.VK_PAGE_UP: + if (viewport.wrapAlignment) + alignPanel.scrollUp(true); + else + alignPanel.setScrollValues(viewport.startRes, + viewport.startSeq + - viewport.endSeq + viewport.startSeq); + break; + + case KeyEvent.VK_PAGE_DOWN: + if (viewport.wrapAlignment) + alignPanel.scrollUp(false); + else + alignPanel.setScrollValues(viewport.startRes, + viewport.startSeq + + viewport.endSeq - viewport.startSeq); + break; + + case KeyEvent.VK_Z: + if (evt.isControlDown()) + { + undoMenuItem_actionPerformed(); + } + break; + + case KeyEvent.VK_Y: + if (evt.isControlDown()) + { + redoMenuItem_actionPerformed(); + } + break; + + case KeyEvent.VK_L: + if (evt.isControlDown()) + { + trimAlignment(true); + } + break; + + case KeyEvent.VK_R: + if (evt.isControlDown()) + { + trimAlignment(false); + } + break; + + case KeyEvent.VK_E: + if (evt.isControlDown()) + { + if (evt.isShiftDown()) + this.removeAllGapsMenuItem_actionPerformed(); + else + removeGappedColumnMenuItem_actionPerformed(); + } + break; + case KeyEvent.VK_I: + if (evt.isControlDown()) + { + if (evt.isAltDown()) + viewport.invertColumnSelection(); + else + this.invertSequenceMenuItem_actionPerformed(); + } + break; + + case KeyEvent.VK_U: + if (evt.isControlDown()) + { + this.deleteGroups_actionPerformed(); + } + break; + + case KeyEvent.VK_T: + if (evt.isControlDown()) + { + newView(); + } + break; + + + } + alignPanel.repaint(); + } + public void keyReleased(KeyEvent evt) + {} + public void keyTyped(KeyEvent evt) + {} + +public void itemStateChanged(ItemEvent evt) + { + if(evt.getSource()==colourTextMenuItem) + colourTextMenuItem_actionPerformed(); + else if(evt.getSource()==wrapMenuItem) + wrapMenuItem_actionPerformed(); + else if(evt.getSource()==scaleAbove) + viewport.setScaleAboveWrapped(scaleAbove.getState()); + else if(evt.getSource()==scaleLeft) + viewport.setScaleLeftWrapped(scaleLeft.getState()); + else if(evt.getSource()==scaleRight) + viewport.setScaleRightWrapped(scaleRight.getState()); + else if(evt.getSource()==seqLimits) + seqLimits_itemStateChanged(); + else if(evt.getSource()==viewBoxesMenuItem) + viewport.setShowBoxes(viewBoxesMenuItem.getState()); + else if(evt.getSource()==viewTextMenuItem) + viewport.setShowText(viewTextMenuItem.getState()); + else if(evt.getSource()==renderGapsMenuItem) + viewport.setRenderGaps(renderGapsMenuItem.getState()); + else if(evt.getSource()==annotationPanelMenuItem) + { + viewport.setShowAnnotation(annotationPanelMenuItem.getState()); + alignPanel.setAnnotationVisible(annotationPanelMenuItem.getState()); + } + else if(evt.getSource()==sequenceFeatures) + { + viewport.showSequenceFeatures(sequenceFeatures.getState()); + alignPanel.seqPanel.seqCanvas.repaint(); + } + else if(evt.getSource()==conservationMenuItem) + conservationMenuItem_actionPerformed(); + else if(evt.getSource()==abovePIDThreshold) + abovePIDThreshold_actionPerformed(); + else if(evt.getSource()==applyToAllGroups) + viewport.setColourAppliesToAllGroups(applyToAllGroups.getState()); + else if(evt.getSource()==autoCalculate) + viewport.autocalculateConsensus = autoCalculate.getState(); + + alignPanel.repaint(); + } + public void actionPerformed(ActionEvent evt) + { + Object source = evt.getSource(); + + if(source==inputText) + inputText_actionPerformed(); + else if(source==loadTree) + loadTree_actionPerformed(); + else if(source==loadApplication) + launchFullApplication(); + else if(source==closeMenuItem) + closeMenuItem_actionPerformed(); + else if(source==copy) + copy_actionPerformed(); + else if(source==undoMenuItem) + undoMenuItem_actionPerformed(); + else if(source==redoMenuItem) + redoMenuItem_actionPerformed(); + else if(source==inputText) + inputText_actionPerformed(); + else if(source==closeMenuItem) + closeMenuItem_actionPerformed(); + else if(source==undoMenuItem) + undoMenuItem_actionPerformed(); + else if(source==redoMenuItem) + redoMenuItem_actionPerformed(); + else if(source==copy) + copy_actionPerformed(); + else if(source==pasteNew) + pasteNew_actionPerformed(); + else if(source==pasteThis) + pasteThis_actionPerformed(); + else if(source==cut) + cut_actionPerformed(); + else if(source==delete) + delete_actionPerformed(); + else if(source==deleteGroups) + deleteGroups_actionPerformed(); + else if(source==selectAllSequenceMenuItem) + selectAllSequenceMenuItem_actionPerformed(); + else if(source==deselectAllSequenceMenuItem) + deselectAllSequenceMenuItem_actionPerformed(); + else if(source==invertSequenceMenuItem) + invertSequenceMenuItem_actionPerformed(); + else if(source==invertColSel) + { viewport.invertColumnSelection(); alignPanel.repaint(); } + else if(source==remove2LeftMenuItem) + trimAlignment(true); + else if(source==remove2RightMenuItem) + trimAlignment(false); + else if(source==removeGappedColumnMenuItem) + removeGappedColumnMenuItem_actionPerformed(); + else if(source==removeAllGapsMenuItem) + removeAllGapsMenuItem_actionPerformed(); + else if(source==findMenuItem) + findMenuItem_actionPerformed(); + else if(source==font) + new FontChooser(alignPanel); + else if (source == newView) + newView(); + else if(source==showColumns) + { + viewport.showAllHiddenColumns(); alignPanel.repaint(); + } + else if(source==showSeqs) + { + viewport.showAllHiddenSeqs(); + } + else if(source == hideColumns) + { + viewport.hideSelectedColumns(); alignPanel.repaint(); + } + else if(source == hideSequences && viewport.getSelectionGroup()!=null) + { + viewport.hideAllSelectedSeqs(); + } + else if(source==featureSettings) + new FeatureSettings(alignPanel); + else if(source==overviewMenuItem) + overviewMenuItem_actionPerformed(); + else if(source==noColourmenuItem) + changeColour(null); + else if(source==clustalColour) + { + abovePIDThreshold.setState(false); + changeColour(new ClustalxColourScheme(viewport.alignment.getSequences(), + viewport.alignment.getWidth())); + } + else if(source==zappoColour) + changeColour(new ZappoColourScheme()); + else if(source==taylorColour) + changeColour(new TaylorColourScheme()); + else if(source==hydrophobicityColour) + changeColour(new HydrophobicColourScheme()); + else if(source==helixColour) + changeColour(new HelixColourScheme()); + else if(source==strandColour) + changeColour(new StrandColourScheme()); + else if(source==turnColour) + changeColour(new TurnColourScheme()); + else if(source==buriedColour) + changeColour(new BuriedColourScheme()); + else if(source==nucleotideColour) + changeColour(new NucleotideColourScheme()); + else if(source==modifyPID) + modifyPID_actionPerformed(); + else if(source==modifyConservation) + modifyConservation_actionPerformed(); + else if(source==userDefinedColour) + new UserDefinedColours(alignPanel, null); + else if(source==PIDColour) + changeColour(new PIDColourScheme()); + else if(source==BLOSUM62Colour) + changeColour(new Blosum62ColourScheme()); + else if(source==annotationColour) + new AnnotationColourChooser(viewport, alignPanel); + else if(source==sortPairwiseMenuItem) + sortPairwiseMenuItem_actionPerformed(); + else if(source==sortIDMenuItem) + sortIDMenuItem_actionPerformed(); + else if(source==sortGroupMenuItem) + sortGroupMenuItem_actionPerformed(); + else if(source==removeRedundancyMenuItem) + removeRedundancyMenuItem_actionPerformed(); + else if(source==pairwiseAlignmentMenuItem) + pairwiseAlignmentMenuItem_actionPerformed(); + else if(source==PCAMenuItem) + PCAMenuItem_actionPerformed(); + else if(source==averageDistanceTreeMenuItem) + averageDistanceTreeMenuItem_actionPerformed(); + else if(source==neighbourTreeMenuItem) + neighbourTreeMenuItem_actionPerformed(); + else if(source==njTreeBlosumMenuItem) + njTreeBlosumMenuItem_actionPerformed(); + else if(source==avDistanceTreeBlosumMenuItem) + avTreeBlosumMenuItem_actionPerformed(); + else if(source==documentation) + documentation_actionPerformed(); + else if(source==about) + about_actionPerformed(); + + } + + public void inputText_actionPerformed() + { + CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this); Frame frame = new Frame(); frame.add(cap); jalview.bin.JalviewLite.addFrame(frame, "Cut & Paste Input", 500, 500); @@ -92,32 +641,110 @@ public class AlignFrame protected void outputText_actionPerformed(ActionEvent e) { - CutAndPasteTransfer cap = new CutAndPasteTransfer(false); + CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this); Frame frame = new Frame(); frame.add(cap); jalview.bin.JalviewLite.addFrame(frame, "Alignment output - " + e.getActionCommand(), 600, 500); - cap.setText(FormatAdapter.formatSequences(e.getActionCommand(), - viewport.getAlignment(). - getSequences())); + cap.setText(new AppletFormatAdapter().formatSequences(e.getActionCommand(), + viewport.getAlignment().getSequences(), + viewport.showJVSuffix)); + } + + void launchFullApplication() + { + StringBuffer url = new StringBuffer(jalviewServletURL); + + url.append("?open="+ + appendProtocol( viewport.applet.getParameter("file") ) ); + + if(viewport.applet.getParameter("features")!=null) + { + url.append( "&features=" ); + url.append( appendProtocol( viewport.applet.getParameter("features") ) ); + } + + if(viewport.applet.getParameter("annotations")!=null) + { + url.append( "&annotations=" ); + url.append( appendProtocol( viewport.applet.getParameter("annotations") ) ); + } + + if(viewport.applet.getParameter("jnetfile")!=null) + { + url.append( "&annotations=" ); + url.append( appendProtocol( viewport.applet.getParameter("jnetfile") ) ); + } + + if(viewport.applet.getParameter("defaultColour")!=null) + { + url.append("&colour=" + + removeWhiteSpace(viewport.applet.getParameter("defaultColour")) + ); + } + + if(viewport.applet.getParameter("userDefinedColour")!=null) + { + url.append( "&colour=" + + removeWhiteSpace( viewport.applet.getParameter("userDefinedColour") ) + ); + } + + showURL(url.toString(), "FULL_APP"); + } + + + String removeWhiteSpace(String colour) + { + StringBuffer sb = new StringBuffer(); + for (int i = 0; i < colour.length(); i++) + { + if (Character.isWhitespace(colour.charAt(i))) + sb.append("%20"); + else + sb.append(colour.charAt(i)); + } + + return sb.toString(); + } + + + String appendProtocol(String url) + { + try{ + new URL(url); + }catch(java.net.MalformedURLException ex) + { + url = viewport.applet.getCodeBase()+url; + } + return url; } - public void closeMenuItem_actionPerformed(ActionEvent e) + public void closeMenuItem_actionPerformed() { - dispose(); + PaintRefresher.RemoveComponent(alignPanel); + PaintRefresher.RemoveComponent(alignPanel.seqPanel.seqCanvas); + PaintRefresher.RemoveComponent(alignPanel.idPanel.idCanvas); + + if(PaintRefresher.components.size()==0 && viewport.applet==null) + System.exit(0); + + this.dispose(); } - Stack historyList = new Stack(); - Stack redoList = new Stack(); + /** + * DOCUMENT ME! + */ void updateEditMenuBar() { - if (historyList.size() > 0) + + if (viewport.historyList.size() > 0) { undoMenuItem.setEnabled(true); - HistoryItem hi = (HistoryItem) historyList.peek(); - undoMenuItem.setLabel("Undo " + hi.getDescription()); + CommandI command = (CommandI) viewport.historyList.peek(); + undoMenuItem.setLabel("Undo " + command.getDescription()); } else { @@ -125,11 +752,12 @@ public class AlignFrame undoMenuItem.setLabel("Undo"); } - if (redoList.size() > 0) + if (viewport.redoList.size() > 0) { redoMenuItem.setEnabled(true); - HistoryItem hi = (HistoryItem) redoList.peek(); - redoMenuItem.setLabel("Redo " + hi.getDescription()); + + CommandI command = (CommandI) viewport.redoList.peek(); + redoMenuItem.setLabel("Redo " + command.getDescription()); } else { @@ -138,74 +766,97 @@ public class AlignFrame } } - public void addHistoryItem(HistoryItem hi) + public void addHistoryItem(CommandI command) { - historyList.push(hi); - updateEditMenuBar(); + if(command.getSize()>0) + { + viewport.historyList.push(command); + viewport.redoList.removeAllElements(); + updateEditMenuBar(); + viewport.hasHiddenColumns = viewport.colSel.getHiddenColumns() != null; + } } - protected void undoMenuItem_actionPerformed(ActionEvent e) + /** + * DOCUMENT ME! + * + * @param e DOCUMENT ME! + */ + protected void undoMenuItem_actionPerformed() { - HistoryItem hi = (HistoryItem) historyList.pop(); - redoList.push(new HistoryItem(hi.getDescription(), viewport.alignment, - HistoryItem.HIDE)); - restoreHistoryItem(hi); + if(viewport.historyList.size()<1) + return; + + CommandI command = (CommandI)viewport.historyList.pop(); + viewport.redoList.push(command); + command.undoCommand(); + + AlignViewport originalSource = getOriginatingSource(command); + + originalSource.hasHiddenColumns = viewport.colSel.getHiddenColumns() != null; + updateEditMenuBar(); + originalSource.firePropertyChange("alignment", null,null); } - protected void redoMenuItem_actionPerformed(ActionEvent e) + /** + * DOCUMENT ME! + * + * @param e DOCUMENT ME! + */ + protected void redoMenuItem_actionPerformed() { - HistoryItem hi = (HistoryItem) redoList.pop(); - restoreHistoryItem(hi); + if(viewport.redoList.size()<1) + return; + + CommandI command = (CommandI) viewport.redoList.pop(); + viewport.historyList.push(command); + command.doCommand(); + + AlignViewport originalSource = getOriginatingSource(command); + originalSource.hasHiddenColumns = viewport.colSel.getHiddenColumns()!=null; + updateEditMenuBar(); - viewport.updateConsensus(); - alignPanel.repaint(); - alignPanel.repaint(); + originalSource.firePropertyChange("alignment", null, null); } - // used by undo and redo - void restoreHistoryItem(HistoryItem hi) + AlignViewport getOriginatingSource(CommandI command) { - if (hi.getType() == HistoryItem.SORT) + AlignViewport originalSource = null; + //For sequence removal and addition, we need to fire + //the property change event FROM the viewport where the + //original alignment was altered + AlignmentI al = null; + if (command instanceof EditCommand) { - for (int i = 0; i < hi.getSequences().size(); i++) + EditCommand editCommand = (EditCommand) command; + al = editCommand.getAlignment(); + Vector comps = (Vector) PaintRefresher.components + .get(viewport.getSequenceSetId()); + for (int i = 0; i < comps.size(); i++) { - viewport.alignment.getSequences().setElementAt(hi.getSequences(). - elementAt(i), i); - } - } - else - { - for (int i = 0; i < hi.getSequences().size(); i++) - { - SequenceI restore = (SequenceI) hi.getSequences().elementAt(i); - if (restore.getLength() == 0) + if (comps.elementAt(i) instanceof AlignmentPanel) { - // log.System.out.println(hi.getHidden().elementAt(i)); - restore.setSequence(hi.getHidden().elementAt(i).toString()); - viewport.alignment.getSequences().insertElementAt( - restore, - hi.getAlignIndex(i)); - } - else - { - restore.setSequence(hi.getHidden().elementAt(i).toString()); - } - } - if (hi.getType() == HistoryItem.PASTE) - { - for (int i = viewport.alignment.getHeight() - 1; - i > hi.getSequences().size() - 1; i--) - { - viewport.alignment.deleteSequence(i); + if (al == ( (AlignmentPanel) comps.elementAt(i)).av.alignment) + { + originalSource = ( (AlignmentPanel) comps.elementAt(i)).av; + break; + } } } } - updateEditMenuBar(); + if (originalSource == null) + { + //The original view is closed, we must validate + //the current view against the closed view first + if (al != null) + PaintRefresher.validateSequences(al, viewport.alignment); - viewport.updateConsensus(); - viewport.updateConservation(); - alignPanel.repaint(); + originalSource = viewport; + } + + + return originalSource; } public void moveSelectedSequences(boolean up) @@ -221,13 +872,13 @@ public class AlignFrame for (int i = 1; i < viewport.alignment.getHeight(); i++) { SequenceI seq = viewport.alignment.getSequenceAt(i); - if (!sg.sequences.contains(seq)) + if (!sg.getSequences(false).contains(seq)) { continue; } SequenceI temp = viewport.alignment.getSequenceAt(i - 1); - if (sg.sequences.contains(temp)) + if (sg.getSequences(false).contains(temp)) { continue; } @@ -241,13 +892,13 @@ public class AlignFrame for (int i = viewport.alignment.getHeight() - 2; i > -1; i--) { SequenceI seq = viewport.alignment.getSequenceAt(i); - if (!sg.sequences.contains(seq)) + if (!sg.getSequences(true).contains(seq)) { continue; } SequenceI temp = viewport.alignment.getSequenceAt(i + 1); - if (sg.sequences.contains(temp)) + if (sg.getSequences(true).contains(temp)) { continue; } @@ -260,8 +911,9 @@ public class AlignFrame alignPanel.repaint(); } - StringBuffer copiedSequences; - protected void copy_actionPerformed(ActionEvent e) + static StringBuffer copiedSequences; + static Vector copiedHiddenColumns; + protected void copy_actionPerformed() { if (viewport.getSelectionGroup() == null) { @@ -271,50 +923,92 @@ public class AlignFrame SequenceGroup sg = viewport.getSelectionGroup(); copiedSequences = new StringBuffer(); Hashtable orderedSeqs = new Hashtable(); - for (int i = 0; i < sg.getSize(); i++) + for (int i = 0; i < sg.getSize(false); i++) { SequenceI seq = sg.getSequenceAt(i); int index = viewport.alignment.findIndex(seq); orderedSeqs.put(index + "", seq); } - int index = 0; - for (int i = 0; i < sg.getSize(); i++) + int index = 0, startRes, endRes; + char ch; + + if (viewport.hasHiddenColumns && viewport.getSelectionGroup() != null) { - SequenceI seq = null; - while (seq == null) + copiedHiddenColumns = new Vector(); + int hiddenOffset = viewport.getSelectionGroup().getStartRes(); + for (int i = 0; i < viewport.getColumnSelection().getHiddenColumns().size(); + i++) { - if (orderedSeqs.containsKey(index + "")) + int[] region = (int[]) + viewport.getColumnSelection().getHiddenColumns().elementAt(i); + + copiedHiddenColumns.addElement(new int[] + {region[0] - hiddenOffset, + region[1] - hiddenOffset}); + } + } + else + copiedHiddenColumns = null; + + + for (int i = 0; i < sg.getSize(false); i++) + { + SequenceI seq = null; + + while (seq == null) { - seq = (SequenceI) orderedSeqs.get(index + ""); - index++; - break; + if (orderedSeqs.containsKey(index + "")) + { + seq = (SequenceI) orderedSeqs.get(index + ""); + index++; + + break; + } + else + { + index++; + } } - else + + //FIND START RES + //Returns residue following index if gap + startRes = seq.findPosition(sg.getStartRes()); + + //FIND END RES + //Need to find the residue preceeding index if gap + endRes = 0; + + for (int j = 0; j < sg.getEndRes()+1 && j < seq.getLength(); j++) + { + ch = seq.getCharAt(j); + if (!jalview.util.Comparison.isGap( (ch))) + { + endRes++; + } + } + + if(endRes>0) { - index++; + endRes += seq.getStart() -1; } - } - copiedSequences.append(seq.getName() + "\t" + - seq.findPosition(sg.getStartRes()) + "\t" - + seq.findPosition(sg.getEndRes()) + "\t" - + - sg.getSequenceAt(i).getSequence(sg.getStartRes(), - sg.getEndRes() + 1) + "\n"); + copiedSequences.append(seq.getName() + "\t" + + startRes + "\t" + + endRes + "\t" + + seq.getSequence(sg.getStartRes(), + sg.getEndRes() + 1) + "\n"); } } - protected void pasteNew_actionPerformed(ActionEvent e) + protected void pasteNew_actionPerformed() { paste(true); } - protected void pasteThis_actionPerformed(ActionEvent e) + protected void pasteThis_actionPerformed() { - addHistoryItem(new HistoryItem("Paste Sequences", viewport.alignment, - HistoryItem.PASTE)); paste(false); } @@ -322,6 +1016,7 @@ public class AlignFrame { try { + if (copiedSequences == null) { return; @@ -334,27 +1029,16 @@ public class AlignFrame String name = st.nextToken(); int start = Integer.parseInt(st.nextToken()); int end = Integer.parseInt(st.nextToken()); - Sequence sequence = new Sequence(name, st.nextToken(), start, end); - - if (!newAlignment) - { - viewport.alignment.addSequence(sequence); - } - else - { - seqs.addElement(sequence); - } + seqs.addElement(new Sequence(name, st.nextToken(), start, end)); + } + SequenceI[] newSeqs = new SequenceI[seqs.size()]; + for (int i = 0; i < seqs.size(); i++) + { + newSeqs[i] = (SequenceI) seqs.elementAt(i); } if (newAlignment) { - SequenceI[] newSeqs = new SequenceI[seqs.size()]; - for (int i = 0; i < seqs.size(); i++) - { - newSeqs[i] = (SequenceI) seqs.elementAt(i); - } - - AlignFrame af = new AlignFrame(new Alignment(newSeqs), applet); String newtitle = new String("Copied sequences"); if (getTitle().startsWith("Copied sequences")) { @@ -364,16 +1048,43 @@ public class AlignFrame { newtitle = newtitle.concat("- from " + getTitle()); } - jalview.bin.JalviewLite.addFrame(af, newtitle, NEW_WINDOW_WIDTH, - NEW_WINDOW_HEIGHT); + AlignFrame af = new AlignFrame(new Alignment(newSeqs), + viewport.applet, + newtitle, + false); + if (copiedHiddenColumns != null) + { + for (int i = 0; i < copiedHiddenColumns.size(); i++) + { + int[] region = (int[]) copiedHiddenColumns.elementAt(i); + af.viewport.hideColumns(region[0], region[1]); + } + } + + + jalview.bin.JalviewLite.addFrame(af, newtitle, DEFAULT_WIDTH, + DEFAULT_HEIGHT); } else { + for (int i = 0; i < newSeqs.length; i++) + { + viewport.alignment.addSequence(newSeqs[i]); + } + + //!newAlignment + addHistoryItem(new EditCommand( + "Add sequences", + EditCommand.PASTE, + newSeqs, + 0, + viewport.alignment.getWidth(), + viewport.alignment) + ); + viewport.setEndSeq(viewport.alignment.getHeight()); viewport.alignment.getWidth(); - viewport.updateConservation(); - viewport.updateConsensus(); - alignPanel.repaint(); + viewport.firePropertyChange("alignment", null, null); } } @@ -382,86 +1093,105 @@ public class AlignFrame } - protected void cut_actionPerformed(ActionEvent e) + protected void cut_actionPerformed() { - copy_actionPerformed(null); - delete_actionPerformed(null); + copy_actionPerformed(); + delete_actionPerformed(); } - protected void delete_actionPerformed(ActionEvent e) + protected void delete_actionPerformed() { - addHistoryItem(new HistoryItem("Delete Sequences", viewport.alignment, - HistoryItem.HIDE)); - if (viewport.getSelectionGroup() == null) + + SequenceGroup sg = viewport.getSelectionGroup(); + if (sg == null) { return; } - SequenceGroup sg = viewport.getSelectionGroup(); - for (int i = 0; i < sg.sequences.size(); i++) + Vector seqs = new Vector(); + SequenceI seq; + for (int i = 0; i < sg.getSize(false); i++) { - SequenceI seq = sg.getSequenceAt(i); - int index = viewport.getAlignment().findIndex(seq); - seq.deleteChars(sg.getStartRes(), sg.getEndRes() + 1); - - if (seq.getSequence().length() < 1) - { - viewport.getAlignment().deleteSequence(seq); - } - else - { - viewport.getAlignment().getSequences().setElementAt(seq, index); - } + seq = sg.getSequenceAt(i); + seqs.addElement(seq); } + + // If the cut affects all sequences, remove highlighted columns + if (sg.getSize(false) == viewport.alignment.getHeight()) + { + viewport.getColumnSelection().removeElements(sg.getStartRes(), + sg.getEndRes() + 1); + } + + + SequenceI [] cut = new SequenceI[seqs.size()]; + for(int i=0; i 0) { - addHistoryItem(new HistoryItem("Remove Left", viewport.alignment, - HistoryItem.HIDE)); - int min = colSel.getMin(); - viewport.getAlignment().trimLeft(min); - colSel.compensateForEdit(0, min); + if(trimLeft) + column = colSel.getMin(); + else + column = colSel.getMax(); + + SequenceI [] seqs; + if(viewport.getSelectionGroup()!=null) + seqs = viewport.getSelectionGroup().getSequencesAsArray(true); + else + seqs = viewport.alignment.getSequencesArray(); + - if (viewport.getSelectionGroup() != null) + TrimRegionCommand trimRegion; + if(trimLeft) { - viewport.getSelectionGroup().adjustForRemoveLeft(min); + trimRegion = new TrimRegionCommand("Remove Left", + TrimRegionCommand.TRIM_LEFT, + seqs, + column, + viewport.alignment, + viewport.colSel, + viewport.selectionGroup); + viewport.setStartRes(0); } + else + { + trimRegion = new TrimRegionCommand("Remove Right", + TrimRegionCommand.TRIM_RIGHT, + seqs, + column, + viewport.alignment, + viewport.colSel, + viewport.selectionGroup); + } + + statusBar.setText("Removed "+trimRegion.getSize()+" columns."); + + + addHistoryItem(trimRegion); Vector groups = viewport.alignment.getGroups(); + for (int i = 0; i < groups.size(); i++) { SequenceGroup sg = (SequenceGroup) groups.elementAt(i); - if (!sg.adjustForRemoveLeft(min)) + + if ( (trimLeft && !sg.adjustForRemoveLeft(column)) + || (!trimLeft && !sg.adjustForRemoveRight(column))) { viewport.alignment.deleteGroup(sg); } } - alignPanel.repaint(); + viewport.firePropertyChange("alignment", null, + viewport.getAlignment().getSequences()); } } - public void remove2RightMenuItem_actionPerformed(ActionEvent e) - { - ColumnSelection colSel = viewport.getColumnSelection(); - if (colSel.size() > 0) - { - addHistoryItem(new HistoryItem("Remove Right", viewport.alignment, - HistoryItem.HIDE)); - int max = colSel.getMax(); - viewport.getAlignment().trimRight(max); - if (viewport.getSelectionGroup() != null) - { - viewport.getSelectionGroup().adjustForRemoveRight(max); - } - Vector groups = viewport.alignment.getGroups(); - for (int i = 0; i < groups.size(); i++) - { - SequenceGroup sg = (SequenceGroup) groups.elementAt(i); - if (!sg.adjustForRemoveRight(max)) - { - viewport.alignment.deleteGroup(sg); - } - } + public void removeGappedColumnMenuItem_actionPerformed() + { + int start = 0, end = viewport.alignment.getWidth()-1; - alignPanel.repaint(); + SequenceI[] seqs; + if (viewport.getSelectionGroup() != null) + { + seqs = viewport.getSelectionGroup().getSequencesAsArray(true); + start = viewport.getSelectionGroup().getStartRes(); + end = viewport.getSelectionGroup().getEndRes(); } + else + seqs = viewport.alignment.getSequencesArray(); - } - public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e) - { - addHistoryItem(new HistoryItem("Remove Gapped Columns", - viewport.alignment, - HistoryItem.HIDE)); - viewport.getAlignment().removeGaps(); - viewport.updateConservation(); - viewport.updateConsensus(); - alignPanel.repaint(); + RemoveGapColCommand removeGapCols = + new RemoveGapColCommand("Remove Gapped Columns", + seqs, + start, end, + viewport.getGapCharacter()); + + addHistoryItem(removeGapCols); + + statusBar.setText("Removed "+removeGapCols.getSize()+" empty columns."); + + //This is to maintain viewport position on first residue + //of first sequence + SequenceI seq = viewport.alignment.getSequenceAt(0); + int startRes = seq.findPosition(viewport.startRes); + // ShiftList shifts; + // viewport.getAlignment().removeGaps(shifts=new ShiftList()); + // edit.alColumnChanges=shifts.getInverse(); + // if (viewport.hasHiddenColumns) + // viewport.getColumnSelection().compensateForEdits(shifts); + viewport.setStartRes(seq.findIndex(startRes)-1); + viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences()); + } - public void removeAllGapsMenuItem_actionPerformed(ActionEvent e) + public void removeAllGapsMenuItem_actionPerformed() { - addHistoryItem(new HistoryItem("Remove Gaps", - viewport.alignment, - HistoryItem.HIDE)); - SequenceI current; - int jSize; - for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++) + int start = 0, end = viewport.alignment.getWidth()-1; + + SequenceI[] seqs; + if (viewport.getSelectionGroup() != null) { - current = viewport.getAlignment().getSequenceAt(i); - jSize = current.getLength(); - for (int j = 0; j < jSize; j++) - { - if (jalview.util.Comparison.isGap(current.getCharAt(j))) - { - current.deleteCharAt(j); - j--; - jSize--; - } - } + seqs = viewport.getSelectionGroup().getSequencesAsArray(true); + start = viewport.getSelectionGroup().getStartRes(); + end = viewport.getSelectionGroup().getEndRes(); } - viewport.updateConservation(); - viewport.updateConsensus(); - alignPanel.repaint(); + else + seqs = viewport.alignment.getSequencesArray(); + + //This is to maintain viewport position on first residue + //of first sequence + SequenceI seq = viewport.alignment.getSequenceAt(0); + int startRes = seq.findPosition(viewport.startRes); + + addHistoryItem(new RemoveGapsCommand("Remove Gaps", + seqs, + start, end, + viewport.getGapCharacter())); + + viewport.setStartRes(seq.findIndex(startRes)-1); + + viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences()); + } - public void findMenuItem_actionPerformed(ActionEvent e) + public void findMenuItem_actionPerformed() { - Finder finder = new Finder(alignPanel); + new Finder(alignPanel); } - public void font_actionPerformed(ActionEvent e) + public void newView() { - Frame frame = new Frame(); - FontChooser fc = new FontChooser(alignPanel, frame); - frame.add(fc); - jalview.bin.JalviewLite.addFrame(frame, "Change Font", 440, 100); + AlignmentI newal; + if (viewport.hasHiddenRows) + newal = new Alignment(viewport.getAlignment(). + getHiddenSequences() + .getFullAlignment(). + getSequencesArray()); + else + newal = new Alignment(viewport.alignment.getSequencesArray()); + + AlignFrame newaf = new AlignFrame(newal, + viewport.applet, + "", + false); + + newaf.viewport.sequenceSetID = alignPanel.av.getSequenceSetId(); + PaintRefresher.Register(alignPanel, alignPanel.av.getSequenceSetId()); + PaintRefresher.Register(newaf.alignPanel, + newaf.alignPanel.av.getSequenceSetId()); + + PaintRefresher.Register(newaf.alignPanel.idPanel.idCanvas, + newaf.alignPanel.av.getSequenceSetId()); + PaintRefresher.Register(newaf.alignPanel.seqPanel.seqCanvas, + newaf.alignPanel.av.getSequenceSetId()); + + Vector comps = (Vector)PaintRefresher.components.get(viewport.getSequenceSetId()); + int viewSize = -1; + for (int i = 0; i < comps.size(); i++) + { + if (comps.elementAt(i) instanceof AlignmentPanel) + viewSize++; + } + + String title = new String(this.getTitle()); + if (title.indexOf("(View") > -1) + title = title.substring(0, title.indexOf("(View")); + + title+= "(View "+viewSize+")"; + + newaf.setTitle(title.toString()); - } - protected void fullSeqId_actionPerformed(ActionEvent e) + newaf.viewport.historyList = viewport.historyList; + newaf.viewport.redoList = viewport.redoList; + + } + + + public void seqLimits_itemStateChanged() { - viewport.setShowFullId(fullSeqId.getState()); + viewport.setShowJVSuffix(seqLimits.getState()); alignPanel.fontChanged(); alignPanel.repaint(); } - protected void colourTextMenuItem_actionPerformed(ActionEvent e) + + protected void colourTextMenuItem_actionPerformed() { viewport.setColourText(colourTextMenuItem.getState()); alignPanel.repaint(); } - protected void wrapMenuItem_actionPerformed(ActionEvent e) + protected void wrapMenuItem_actionPerformed() { viewport.setWrapAlignment(wrapMenuItem.getState()); alignPanel.setWrapAlignment(wrapMenuItem.getState()); @@ -605,54 +1415,8 @@ public class AlignFrame alignPanel.repaint(); } - protected void scaleAbove_actionPerformed(ActionEvent e) - { - viewport.setScaleAboveWrapped(scaleAbove.getState()); - alignPanel.repaint(); - } - - protected void scaleLeft_actionPerformed(ActionEvent e) - { - viewport.setScaleLeftWrapped(scaleLeft.getState()); - alignPanel.repaint(); - } - - protected void scaleRight_actionPerformed(ActionEvent e) - { - viewport.setScaleRightWrapped(scaleRight.getState()); - alignPanel.repaint(); - } - - public void viewBoxesMenuItem_actionPerformed(ActionEvent e) - { - viewport.setShowBoxes(viewBoxesMenuItem.getState()); - alignPanel.repaint(); - } - - public void viewTextMenuItem_actionPerformed(ActionEvent e) - { - viewport.setShowText(viewTextMenuItem.getState()); - alignPanel.repaint(); - } - - protected void renderGapsMenuItem_actionPerformed(ActionEvent e) - { - viewport.setRenderGaps(renderGapsMenuItem.getState()); - alignPanel.repaint(); - } - - public void annotationPanelMenuItem_actionPerformed(ActionEvent e) - { - if (annotationPanelMenuItem.getState() && viewport.getWrapAlignment()) - { - annotationPanelMenuItem.setState(false); - return; - } - viewport.setShowAnnotation(annotationPanelMenuItem.getState()); - alignPanel.setAnnotationVisible(annotationPanelMenuItem.getState()); - } - public void overviewMenuItem_actionPerformed(ActionEvent e) + public void overviewMenuItem_actionPerformed() { if (alignPanel.overviewPanel != null) { @@ -680,122 +1444,53 @@ public class AlignFrame } - protected void noColourmenuItem_actionPerformed(ActionEvent e) - { - changeColour(null); - } - - public void clustalColour_actionPerformed(ActionEvent e) - { - abovePIDThreshold.setState(false); - changeColour(new ClustalxColourScheme(viewport.alignment.getSequences(), - viewport.alignment.getWidth())); - } - - public void zappoColour_actionPerformed(ActionEvent e) - { - changeColour(new ZappoColourScheme()); - } - - public void taylorColour_actionPerformed(ActionEvent e) - { - changeColour(new TaylorColourScheme()); - } - - public void hydrophobicityColour_actionPerformed(ActionEvent e) - { - changeColour(new HydrophobicColourScheme()); - } - - public void helixColour_actionPerformed(ActionEvent e) - { - changeColour(new HelixColourScheme()); - } - - public void strandColour_actionPerformed(ActionEvent e) - { - changeColour(new StrandColourScheme()); - } - - public void turnColour_actionPerformed(ActionEvent e) - { - changeColour(new TurnColourScheme()); - } - - public void buriedColour_actionPerformed(ActionEvent e) - { - changeColour(new BuriedColourScheme()); - } - - public void nucleotideColour_actionPerformed(ActionEvent e) - { - changeColour(new NucleotideColourScheme()); - } - - protected void applyToAllGroups_actionPerformed(ActionEvent e) - { - viewport.setColourAppliesToAllGroups(applyToAllGroups.getState()); - } void changeColour(ColourSchemeI cs) { int threshold = 0; - if (viewport.getAbovePIDThreshold()) + if(cs!=null) { - threshold = SliderPanel.setPIDSliderSource(alignPanel, cs, "Background"); - - if (cs instanceof ResidueColourScheme) + if (viewport.getAbovePIDThreshold()) { - ( (ResidueColourScheme) cs).setThreshold(threshold); + threshold = SliderPanel.setPIDSliderSource(alignPanel, cs, "Background"); + + cs.setThreshold(threshold, viewport.getIgnoreGapsConsensus()); + + viewport.setGlobalColourScheme(cs); } - else if (cs instanceof ScoreColourScheme) + else { - ( (ScoreColourScheme) cs).setThreshold(threshold); + cs.setThreshold(0, viewport.getIgnoreGapsConsensus()); } - viewport.setGlobalColourScheme(cs); - } - else if (cs instanceof ResidueColourScheme) - { - ( (ResidueColourScheme) cs).setThreshold(0); - } - else if (cs instanceof ScoreColourScheme) - { - ( (ScoreColourScheme) cs).setThreshold(0); - } - - if (viewport.getConservationSelected()) - { - ConservationColourScheme ccs = null; - - Alignment al = (Alignment) viewport.alignment; - Conservation c = new Conservation("All", - ResidueProperties.propHash, 3, - al.getSequences(), 0, - al.getWidth() - 1); + if (viewport.getConservationSelected()) + { - c.calculate(); - c.verdict(false, viewport.ConsPercGaps); + Alignment al = (Alignment) viewport.alignment; + Conservation c = new Conservation("All", + ResidueProperties.propHash, 3, + al.getSequences(), 0, + al.getWidth() - 1); - ccs = new ConservationColourScheme(c, cs); + c.calculate(); + c.verdict(false, viewport.ConsPercGaps); - // MUST NOTIFY THE COLOURSCHEME OF CONSENSUS! - ccs.setConsensus(viewport.vconsensus); - viewport.setGlobalColourScheme(ccs); + cs.setConservation(c); - SliderPanel.setConservationSlider(alignPanel, ccs, "Background"); + cs.setConservationInc(SliderPanel.setConservationSlider(alignPanel, cs, + "Background")); - } - else - { - // MUST NOTIFY THE COLOURSCHEME OF CONSENSUS! - if (cs != null) + } + else { - cs.setConsensus(viewport.vconsensus); + cs.setConservation(null); } - viewport.setGlobalColourScheme(cs); + + cs.setConsensus(viewport.hconsensus); + } + viewport.setGlobalColourScheme(cs); if (viewport.getColourAppliesToAllGroups()) { @@ -804,9 +1499,14 @@ public class AlignFrame { SequenceGroup sg = (SequenceGroup) groups.elementAt(i); + if(cs==null) + { + sg.cs = null; + continue; + } if (cs instanceof ClustalxColourScheme) { - sg.cs = new ClustalxColourScheme(sg.sequences, sg.getWidth()); + sg.cs = new ClustalxColourScheme(sg.getSequences(true), sg.getWidth()); } else { @@ -821,43 +1521,36 @@ public class AlignFrame } } - if (viewport.getAbovePIDThreshold()) + if (viewport.getAbovePIDThreshold() + || cs instanceof PIDColourScheme + || cs instanceof Blosum62ColourScheme) { - if (sg.cs instanceof ResidueColourScheme) - { - ( (ResidueColourScheme) sg.cs).setThreshold(threshold); - } - else if (sg.cs instanceof ScoreColourScheme) - { - ( (ScoreColourScheme) sg.cs).setThreshold(threshold); - } - - sg.cs.setConsensus(AAFrequency.calculate(sg.sequences, 0, sg.getWidth())); + sg.cs.setThreshold(threshold, viewport.getIgnoreGapsConsensus()); + sg.cs.setConsensus(AAFrequency.calculate(sg.getSequences(true), 0, sg.getWidth())); } + else + sg.cs.setThreshold(0, viewport.getIgnoreGapsConsensus()); if (viewport.getConservationSelected()) { Conservation c = new Conservation("Group", ResidueProperties.propHash, 3, - sg.sequences, 0, + sg.getSequences(true), 0, viewport.alignment.getWidth() - 1); c.calculate(); c.verdict(false, viewport.ConsPercGaps); - ConservationColourScheme ccs = new ConservationColourScheme(c, sg.cs); - - // MUST NOTIFY THE COLOURSCHEME OF CONSENSUS! - ccs.setConsensus(AAFrequency.calculate(sg.sequences, 0, sg.getWidth())); - sg.cs = ccs; + sg.cs.setConservation(c); } else { - // MUST NOTIFY THE COLOURSCHEME OF CONSENSUS! - sg.cs.setConsensus(AAFrequency.calculate(sg.sequences, 0, sg.getWidth())); + sg.cs.setConservation(null); + sg.cs.setThreshold(0, viewport.getIgnoreGapsConsensus()); } } } + if (alignPanel.getOverviewPanel() != null) { alignPanel.getOverviewPanel().updateOverviewImage(); @@ -866,9 +1559,11 @@ public class AlignFrame alignPanel.repaint(); } - protected void modifyPID_actionPerformed(ActionEvent e) + + + protected void modifyPID_actionPerformed() { - if (viewport.getAbovePIDThreshold()) + if (viewport.getAbovePIDThreshold() && viewport.globalColourScheme!=null) { SliderPanel.setPIDSliderSource(alignPanel, viewport.getGlobalColourScheme(), "Background"); @@ -876,9 +1571,9 @@ public class AlignFrame } } - protected void modifyConservation_actionPerformed(ActionEvent e) + protected void modifyConservation_actionPerformed() { - if (viewport.getConservationSelected()) + if (viewport.getConservationSelected() && viewport.globalColourScheme!=null) { SliderPanel.setConservationSlider(alignPanel, viewport.globalColourScheme, "Background"); @@ -886,114 +1581,98 @@ public class AlignFrame } } - protected void conservationMenuItem_actionPerformed(ActionEvent e) + protected void conservationMenuItem_actionPerformed() { viewport.setConservationSelected(conservationMenuItem.getState()); viewport.setAbovePIDThreshold(false); abovePIDThreshold.setState(false); - ColourSchemeI cs = viewport.getGlobalColourScheme(); - if (cs instanceof ConservationColourScheme) - { - changeColour( ( (ConservationColourScheme) cs).cs); - } - else - { - changeColour(cs); - } + changeColour(viewport.getGlobalColourScheme()); - modifyConservation_actionPerformed(null); + modifyConservation_actionPerformed(); } - public void abovePIDThreshold_actionPerformed(ActionEvent e) + public void abovePIDThreshold_actionPerformed() { viewport.setAbovePIDThreshold(abovePIDThreshold.getState()); conservationMenuItem.setState(false); viewport.setConservationSelected(false); - ColourSchemeI cs = viewport.getGlobalColourScheme(); - - if (cs instanceof ConservationColourScheme) - { - changeColour( ( (ConservationColourScheme) cs).cs); - } - else - { - changeColour(cs); - } - - modifyPID_actionPerformed(null); - } + changeColour(viewport.getGlobalColourScheme()); - public void userDefinedColour_actionPerformed(ActionEvent e) - { - UserDefinedColours chooser = new UserDefinedColours(alignPanel, null); + modifyPID_actionPerformed(); } - public void PIDColour_actionPerformed(ActionEvent e) - { - changeColour(new PIDColourScheme()); - } - public void BLOSUM62Colour_actionPerformed(ActionEvent e) - { - changeColour(new Blosum62ColourScheme()); - } - public void sortPairwiseMenuItem_actionPerformed(ActionEvent e) + public void sortPairwiseMenuItem_actionPerformed() { - addHistoryItem(new HistoryItem("Pairwise Sort", viewport.alignment, - HistoryItem.SORT)); + SequenceI [] oldOrder = viewport.getAlignment().getSequencesArray(); AlignmentSorter.sortByPID(viewport.getAlignment(), viewport.getAlignment().getSequenceAt(0)); + addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder, viewport.alignment)); alignPanel.repaint(); } - public void sortIDMenuItem_actionPerformed(ActionEvent e) + public void sortIDMenuItem_actionPerformed() { - addHistoryItem(new HistoryItem("ID Sort", viewport.alignment, - HistoryItem.SORT)); + // addHistoryItem(new HistoryItem("ID Sort", viewport.alignment, + // HistoryItem.SORT)); AlignmentSorter.sortByID(viewport.getAlignment()); alignPanel.repaint(); } - public void sortGroupMenuItem_actionPerformed(ActionEvent e) + public void sortGroupMenuItem_actionPerformed() { - addHistoryItem(new HistoryItem("Group Sort", viewport.alignment, - HistoryItem.SORT)); + // addHistoryItem(new HistoryItem("Group Sort", viewport.alignment, + // HistoryItem.SORT)); AlignmentSorter.sortByGroup(viewport.getAlignment()); - AlignmentSorter.sortGroups(viewport.getAlignment()); alignPanel.repaint(); + } - public void removeRedundancyMenuItem_actionPerformed(ActionEvent e) + public void removeRedundancyMenuItem_actionPerformed() { - RedundancyPanel sp = new RedundancyPanel(alignPanel); - Frame frame = new Frame(); - frame.add(sp); - jalview.bin.JalviewLite.addFrame(frame, "Redundancy threshold selection", - 400, 120); - + new RedundancyPanel(alignPanel); } - public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e) + public void pairwiseAlignmentMenuItem_actionPerformed() { - if (viewport.getSelectionGroup().getSize() > 1) + if (viewport.getSelectionGroup()!=null + && viewport.getSelectionGroup().getSize(false) > 1) { Frame frame = new Frame(); - frame.add(new PairwiseAlignPanel(viewport)); + frame.add(new PairwiseAlignPanel(alignPanel)); jalview.bin.JalviewLite.addFrame(frame, "Pairwise Alignment", 600, 500); } } - public void PCAMenuItem_actionPerformed(ActionEvent e) + public void PCAMenuItem_actionPerformed() { + //are the sequences aligned? + if (!viewport.alignment.isAligned()) + { + SequenceI current; + int Width = viewport.getAlignment().getWidth(); + + for (int i = 0; i < viewport.getAlignment().getSequences().size(); + i++) + { + current = viewport.getAlignment().getSequenceAt(i); + + if (current.getLength() < Width) + { + current.insertCharAt(Width - 1, viewport.getGapCharacter()); + } + } + alignPanel.repaint(); + } if ( (viewport.getSelectionGroup() != null && - viewport.getSelectionGroup().getSize() < 4 && - viewport.getSelectionGroup().getSize() > 0) + viewport.getSelectionGroup().getSize(false) < 4 && + viewport.getSelectionGroup().getSize(false) > 0) || viewport.getAlignment().getHeight() < 4) { return; @@ -1001,11 +1680,7 @@ public class AlignFrame try { - PCAPanel pcaPanel = new PCAPanel(viewport, null); - Frame frame = new Frame(); - frame.add(pcaPanel); - jalview.bin.JalviewLite.addFrame(frame, "Principal component analysis", - 400, 400); + new PCAPanel(viewport); } catch (java.lang.OutOfMemoryError ex) { @@ -1013,22 +1688,22 @@ public class AlignFrame } - public void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e) + public void averageDistanceTreeMenuItem_actionPerformed() { NewTreePanel("AV", "PID", "Average distance tree using PID"); } - public void neighbourTreeMenuItem_actionPerformed(ActionEvent e) + public void neighbourTreeMenuItem_actionPerformed() { NewTreePanel("NJ", "PID", "Neighbour joining tree using PID"); } - protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e) + protected void njTreeBlosumMenuItem_actionPerformed() { NewTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62"); } - protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e) + protected void avTreeBlosumMenuItem_actionPerformed() { NewTreePanel("AV", "BL", "Average distance tree using BLOSUM62PID"); } @@ -1038,26 +1713,56 @@ public class AlignFrame //are the sequences aligned? if (!viewport.alignment.isAligned()) { - return; - } + SequenceI current; + int Width = viewport.getAlignment().getWidth(); + + for (int i = 0; i < viewport.getAlignment().getSequences().size(); + i++) + { + current = viewport.getAlignment().getSequenceAt(i); + + if (current.getLength() < Width) + { + current.insertCharAt(Width - 1, viewport.getGapCharacter()); + } + } + alignPanel.repaint(); - final TreePanel tp; - if (viewport.getSelectionGroup() != null && - viewport.getSelectionGroup().getSize() > 3) - { - tp = new TreePanel(viewport, viewport.getSelectionGroup().sequences, type, - pwType, - 0, viewport.alignment.getWidth()); } - else + + if ( (viewport.getSelectionGroup() != null && + viewport.getSelectionGroup().getSize(false) > 1) + || (viewport.getSelectionGroup() == null + && viewport.alignment.getHeight() > 1)) { - tp = new TreePanel(viewport, viewport.getAlignment().getSequences(), - type, pwType, 0, viewport.alignment.getWidth()); + final TreePanel tp = new TreePanel(viewport, + type, + pwType); + + addTreeMenuItem(tp, title); + + jalview.bin.JalviewLite.addFrame(tp, title, 600, 500); } + } - addTreeMenuItem(tp, title); + void loadTree_actionPerformed() + { + CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this); + cap.setText("Paste your Newick tree file here."); + cap.treeImport = true; + Frame frame = new Frame(); + frame.add(cap); + jalview.bin.JalviewLite.addFrame(frame, "Paste Newick file ", 400, 300); + } - jalview.bin.JalviewLite.addFrame(tp, title, 600, 500); + public void loadTree(jalview.io.NewickFile tree, String treeFile) + { + TreePanel tp = new TreePanel(viewport, + treeFile, + "From File - ", + tree); + jalview.bin.JalviewLite.addFrame(tp, treeFile, 600, 500); + addTreeMenuItem(tp, treeFile); } void addTreeMenuItem(final TreePanel treePanel, String title) @@ -1066,10 +1771,10 @@ public class AlignFrame sortByTreeMenu.add(item); item.addActionListener(new java.awt.event.ActionListener() { - public void actionPerformed(ActionEvent e) + public void actionPerformed(ActionEvent evt) { - addHistoryItem(new HistoryItem("Sort", viewport.alignment, - HistoryItem.SORT)); + // addHistoryItem(new HistoryItem("Sort", viewport.alignment, + // HistoryItem.SORT)); AlignmentSorter.sortByTree(viewport.getAlignment(), treePanel.getTree()); alignPanel.repaint(); } @@ -1084,18 +1789,20 @@ public class AlignFrame }); } - protected void documentation_actionPerformed(ActionEvent e) + protected void documentation_actionPerformed() { - - jalview.bin.JalviewLite.showURL("http://www.jalview.org"); - + showURL("http://www.jalview.org/help.html", "HELP"); } - protected void about_actionPerformed(ActionEvent e) + protected void about_actionPerformed() { - class AboutPanel - extends Canvas + + class AboutPanel extends Canvas { + String version; + public AboutPanel(String version) + { this.version = version; } + public void paint(Graphics g) { g.setColor(Color.white); @@ -1106,7 +1813,7 @@ public class AlignFrame int y = 5, x = 7; g.setColor(Color.black); g.setFont(new Font("Helvetica", Font.BOLD, 14)); - g.drawString("JalView - Release 2.0", 200, y += fh); + g.drawString("Jalview - Release "+version, 200, y += fh); g.setFont(new Font("Helvetica", Font.PLAIN, 12)); g.drawString("Authors: Michele Clamp, James Cuff, Steve Searle, Andrew Waterhouse, Jim Procter & Geoff Barton.", x, y += fh * 2); @@ -1118,13 +1825,595 @@ public class AlignFrame g.drawString("If you use JalView, please cite:", x, y += fh + 8); g.drawString("\"Clamp, M., Cuff, J., Searle, S. M. and Barton, G. J. (2004), The Jalview Java Alignment Editor\"", x, y += fh); - g.drawString("Bioinformatics, 2004 12;426-7.", x, y += fh); + g.drawString("Bioinformatics, 2004 20;426-7.", x, y += fh); + } + } + + String version = "test"; + java.net.URL url = getClass().getResource("/.build_properties"); + if (url != null) + { + try + { + BufferedReader reader = new BufferedReader(new InputStreamReader( + url.openStream())); + String line; + while ( (line = reader.readLine()) != null) + { + if (line.indexOf("VERSION") > -1) + { + version = line.substring(line.indexOf("=") + 1); + } + } + } + catch (Exception ex) + { + ex.printStackTrace(); } } + Frame frame = new Frame(); - frame.add(new AboutPanel()); + frame.add(new AboutPanel(version)); jalview.bin.JalviewLite.addFrame(frame, "Jalview", 580, 200); } + + public void showURL(String url, String target) + { + if (viewport.applet == null) + { + System.out.println("Not running as applet - no browser available."); + } + else + { + try + { + System.out.println("Show url: "+url); + viewport.applet.getAppletContext().showDocument(new java.net.URL(url), + target); + } + catch (Exception ex) + { + ex.printStackTrace(); + } + } + } + + + ////////////////////////////////////////////////////////////////////////////////// + //JBuilder Graphics here + + protected MenuBar alignFrameMenuBar = new MenuBar(); + protected Menu fileMenu = new Menu("File"); + protected MenuItem loadApplication = new MenuItem("View in Full Application"); + protected MenuItem loadTree = new MenuItem("Load Associated Tree"); + protected MenuItem closeMenuItem = new MenuItem("Close"); + protected Menu editMenu = new Menu("Edit"); + protected Menu viewMenu = new Menu("View"); + protected Menu colourMenu = new Menu("Colour"); + protected Menu calculateMenu = new Menu("Calculate"); + protected MenuItem selectAllSequenceMenuItem = new MenuItem("Select all"); + protected MenuItem deselectAllSequenceMenuItem = new MenuItem("Deselect All"); + protected MenuItem invertSequenceMenuItem = new MenuItem("Invert Selection"); + protected MenuItem remove2LeftMenuItem = new MenuItem(); + protected MenuItem remove2RightMenuItem = new MenuItem(); + protected MenuItem removeGappedColumnMenuItem = new MenuItem(); + protected MenuItem removeAllGapsMenuItem = new MenuItem(); + protected CheckboxMenuItem viewBoxesMenuItem = new CheckboxMenuItem(); + protected CheckboxMenuItem viewTextMenuItem = new CheckboxMenuItem(); + protected MenuItem sortPairwiseMenuItem = new MenuItem(); + protected MenuItem sortIDMenuItem = new MenuItem(); + protected MenuItem sortGroupMenuItem = new MenuItem(); + protected MenuItem removeRedundancyMenuItem = new MenuItem(); + protected MenuItem pairwiseAlignmentMenuItem = new MenuItem(); + protected MenuItem PCAMenuItem = new MenuItem(); + protected MenuItem averageDistanceTreeMenuItem = new MenuItem(); + protected MenuItem neighbourTreeMenuItem = new MenuItem(); + BorderLayout borderLayout1 = new BorderLayout(); + public Label statusBar = new Label(); + protected Menu outputTextboxMenu = new Menu(); + protected MenuItem clustalColour = new MenuItem(); + protected MenuItem zappoColour = new MenuItem(); + protected MenuItem taylorColour = new MenuItem(); + protected MenuItem hydrophobicityColour = new MenuItem(); + protected MenuItem helixColour = new MenuItem(); + protected MenuItem strandColour = new MenuItem(); + protected MenuItem turnColour = new MenuItem(); + protected MenuItem buriedColour = new MenuItem(); + protected MenuItem userDefinedColour = new MenuItem(); + protected MenuItem PIDColour = new MenuItem(); + protected MenuItem BLOSUM62Colour = new MenuItem(); + MenuItem njTreeBlosumMenuItem = new MenuItem(); + MenuItem avDistanceTreeBlosumMenuItem = new MenuItem(); + protected CheckboxMenuItem annotationPanelMenuItem = new CheckboxMenuItem(); + protected CheckboxMenuItem colourTextMenuItem = new CheckboxMenuItem(); + MenuItem overviewMenuItem = new MenuItem(); + protected MenuItem undoMenuItem = new MenuItem(); + protected MenuItem redoMenuItem = new MenuItem(); + protected CheckboxMenuItem conservationMenuItem = new CheckboxMenuItem(); + MenuItem noColourmenuItem = new MenuItem(); + protected CheckboxMenuItem wrapMenuItem = new CheckboxMenuItem(); + protected CheckboxMenuItem renderGapsMenuItem = new CheckboxMenuItem(); + MenuItem findMenuItem = new MenuItem(); + protected CheckboxMenuItem abovePIDThreshold = new CheckboxMenuItem(); + protected MenuItem nucleotideColour = new MenuItem(); + MenuItem deleteGroups = new MenuItem(); + MenuItem delete = new MenuItem(); + MenuItem copy = new MenuItem(); + MenuItem cut = new MenuItem(); + Menu pasteMenu = new Menu(); + MenuItem pasteNew = new MenuItem(); + MenuItem pasteThis = new MenuItem(); + protected CheckboxMenuItem applyToAllGroups = new CheckboxMenuItem(); + protected MenuItem font = new MenuItem(); + protected CheckboxMenuItem scaleAbove = new CheckboxMenuItem(); + protected CheckboxMenuItem scaleLeft = new CheckboxMenuItem(); + protected CheckboxMenuItem scaleRight = new CheckboxMenuItem(); + MenuItem modifyPID = new MenuItem(); + MenuItem modifyConservation = new MenuItem(); + protected CheckboxMenuItem autoCalculate + = new CheckboxMenuItem("Autocalculate Consensus", true); + protected Menu sortByTreeMenu = new Menu(); + Menu sort = new Menu(); + Menu calculate = new Menu(); + MenuItem inputText = new MenuItem(); + Menu helpMenu = new Menu(); + MenuItem documentation = new MenuItem(); + MenuItem about = new MenuItem(); + protected CheckboxMenuItem seqLimits = new CheckboxMenuItem(); + Panel embeddedMenu; + Label embeddedEdit; + Label embeddedSelect; + Label embeddedView; + Label embeddedFormat; + Label embeddedColour; + Label embeddedFile; + Label embeddedHelp; + Label embeddedCalculate; + FlowLayout flowLayout1; + + private void jbInit() throws Exception { + + setMenuBar(alignFrameMenuBar); + + MenuItem item; + + // dynamically fill save as menu with available formats + for (int i = 0; i < jalview.io.AppletFormatAdapter.WRITEABLE_FORMATS.length; i++) + { + + item = new MenuItem( jalview.io.AppletFormatAdapter.WRITEABLE_FORMATS[i]); + + item.addActionListener(new java.awt.event.ActionListener() + { + public void actionPerformed(ActionEvent e) + { + outputText_actionPerformed(e); + } + }); + + outputTextboxMenu.add(item); + } + closeMenuItem.addActionListener(this); + loadApplication.addActionListener(this); + + loadTree.addActionListener(this); + selectAllSequenceMenuItem.addActionListener(this); + deselectAllSequenceMenuItem.addActionListener(this); + invertSequenceMenuItem.addActionListener(this); + remove2LeftMenuItem.setLabel("Remove Left"); + remove2LeftMenuItem.addActionListener(this); + remove2RightMenuItem.setLabel("Remove Right"); + remove2RightMenuItem.addActionListener(this); + removeGappedColumnMenuItem.setLabel("Remove Empty Columns"); + removeGappedColumnMenuItem.addActionListener(this); + removeAllGapsMenuItem.setLabel("Remove All Gaps"); + removeAllGapsMenuItem.addActionListener(this); + viewBoxesMenuItem.setLabel("Boxes"); + viewBoxesMenuItem.setState(true); + viewBoxesMenuItem.addItemListener(this); + viewTextMenuItem.setLabel("Text"); + viewTextMenuItem.setState(true); + viewTextMenuItem.addItemListener(this); + sortPairwiseMenuItem.setLabel("by Pairwise Identity"); + sortPairwiseMenuItem.addActionListener(this); + sortIDMenuItem.setLabel("by ID"); + sortIDMenuItem.addActionListener(this); + sortGroupMenuItem.setLabel("by Group"); + sortGroupMenuItem.addActionListener(this); + removeRedundancyMenuItem.setLabel("Remove Redundancy..."); + removeRedundancyMenuItem.addActionListener(this); + pairwiseAlignmentMenuItem.setLabel("Pairwise Alignments..."); + pairwiseAlignmentMenuItem.addActionListener(this); + PCAMenuItem.setLabel("Principal Component Analysis"); + PCAMenuItem.addActionListener(this); + averageDistanceTreeMenuItem.setLabel( + "Average Distance Using % Identity"); + averageDistanceTreeMenuItem.addActionListener(this); + neighbourTreeMenuItem.setLabel("Neighbour Joining Using % Identity"); + neighbourTreeMenuItem.addActionListener(this); + alignFrameMenuBar.setFont(new java.awt.Font("Verdana", 0, 11)); + statusBar.setBackground(Color.white); + statusBar.setFont(new java.awt.Font("Verdana", 0, 11)); + statusBar.setText("Status bar"); + outputTextboxMenu.setLabel("Output to Textbox"); + clustalColour.setLabel("Clustalx"); + + clustalColour.addActionListener(this); + zappoColour.setLabel("Zappo"); + zappoColour.addActionListener(this); + taylorColour.setLabel("Taylor"); + taylorColour.addActionListener(this); + hydrophobicityColour.setLabel("Hydrophobicity"); + hydrophobicityColour.addActionListener(this); + helixColour.setLabel("Helix Propensity"); + helixColour.addActionListener(this); + strandColour.setLabel("Strand Propensity"); + strandColour.addActionListener(this); + turnColour.setLabel("Turn Propensity"); + turnColour.addActionListener(this); + buriedColour.setLabel("Buried Index"); + buriedColour.addActionListener(this); + userDefinedColour.setLabel("User Defined..."); + userDefinedColour.addActionListener(this); + PIDColour.setLabel("Percentage Identity"); + PIDColour.addActionListener(this); + BLOSUM62Colour.setLabel("BLOSUM62 Score"); + BLOSUM62Colour.addActionListener(this); + avDistanceTreeBlosumMenuItem.setLabel( + "Average Distance Using BLOSUM62"); + avDistanceTreeBlosumMenuItem.addActionListener(this); + njTreeBlosumMenuItem.setLabel("Neighbour Joining Using BLOSUM62"); + njTreeBlosumMenuItem.addActionListener(this); + annotationPanelMenuItem.setLabel("Show Annotations"); + annotationPanelMenuItem.addItemListener(this); + colourTextMenuItem.setLabel("Colour Text"); + colourTextMenuItem.addItemListener(this); + overviewMenuItem.setLabel("Overview Window"); + overviewMenuItem.addActionListener(this); + undoMenuItem.setEnabled(false); + undoMenuItem.setLabel("Undo"); + undoMenuItem.addActionListener(this); + redoMenuItem.setEnabled(false); + redoMenuItem.setLabel("Redo"); + redoMenuItem.addActionListener(this); + conservationMenuItem.setLabel("by Conservation"); + conservationMenuItem.addItemListener(this); + noColourmenuItem.setLabel("None"); + noColourmenuItem.addActionListener(this); + wrapMenuItem.setLabel("Wrap"); + wrapMenuItem.addItemListener(this); + renderGapsMenuItem.setLabel("Show Gaps"); + renderGapsMenuItem.setState(true); + renderGapsMenuItem.addItemListener(this); + findMenuItem.setLabel("Find..."); + findMenuItem.addActionListener(this); + abovePIDThreshold.setLabel("Above Identity Threshold"); + abovePIDThreshold.addItemListener(this); + nucleotideColour.setLabel("Nucleotide"); + nucleotideColour.addActionListener(this); + deleteGroups.setLabel("Undefine Groups"); + deleteGroups.addActionListener(this); + copy.setLabel("Copy"); + copy.addActionListener(this); + cut.setLabel("Cut"); + cut.addActionListener(this); + delete.setLabel("Delete"); + delete.addActionListener(this); + pasteMenu.setLabel("Paste"); + pasteNew.setLabel("To New Alignment"); + pasteNew.addActionListener(this); + pasteThis.setLabel("Add To This Alignment"); + pasteThis.addActionListener(this); + applyToAllGroups.setLabel("Apply Colour To All Groups"); + applyToAllGroups.setState(true); + applyToAllGroups.addItemListener(this); + font.setLabel("Font..."); + font.addActionListener(this); + scaleAbove.setLabel("Scale Above"); + scaleAbove.setState(true); + scaleAbove.setEnabled(false); + scaleAbove.addItemListener(this); + scaleLeft.setEnabled(false); + scaleLeft.setState(true); + scaleLeft.setLabel("Scale Left"); + scaleLeft.addItemListener(this); + scaleRight.setEnabled(false); + scaleRight.setState(true); + scaleRight.setLabel("Scale Right"); + scaleRight.addItemListener(this); + modifyPID.setLabel("Modify Identity Threshold..."); + modifyPID.addActionListener(this); + modifyConservation.setLabel("Modify Conservation Threshold..."); + modifyConservation.addActionListener(this); + sortByTreeMenu.setLabel("By Tree Order"); + sort.setLabel("Sort"); + calculate.setLabel("Calculate Tree"); + autoCalculate.addItemListener(this); + inputText.setLabel("Input from textbox"); + inputText.addActionListener(this); + + helpMenu.setLabel("Help"); + documentation.setLabel("Documentation"); + documentation.addActionListener(this); + + about.setLabel("About..."); + about.addActionListener(this); + seqLimits.setState(true); + seqLimits.setLabel("Show Sequence Limits"); + seqLimits.addItemListener(this); + featureSettings.setLabel("Feature Settings..."); + featureSettings.addActionListener(this); + sequenceFeatures.setLabel("Sequence Features"); + sequenceFeatures.addItemListener(this); + sequenceFeatures.setState(false); + annotationColour.setLabel("by Annotation..."); + annotationColour.addActionListener(this); + invertSequenceMenuItem.setLabel("Invert Sequence Selection"); + invertColSel.setLabel("Invert Column Selection"); + menu1.setLabel("Show"); + showColumns.setLabel("All Columns "); + showSeqs.setLabel("All Sequences"); + menu2.setLabel("Hide"); + hideColumns.setLabel("Selected Columns"); + hideSequences.setLabel("Selected Sequences"); + invertColSel.addActionListener(this); + showColumns.addActionListener(this); + showSeqs.addActionListener(this); + hideColumns.addActionListener(this); + hideSequences.addActionListener(this); + formatMenu.setLabel("Format"); + selectMenu.setLabel("Select"); + newView.setLabel("New View"); + newView.addActionListener(this); + alignFrameMenuBar.add(fileMenu); + alignFrameMenuBar.add(editMenu); + alignFrameMenuBar.add(selectMenu); + alignFrameMenuBar.add(viewMenu); + alignFrameMenuBar.add(formatMenu); + alignFrameMenuBar.add(colourMenu); + alignFrameMenuBar.add(calculateMenu); + alignFrameMenuBar.add(helpMenu); + fileMenu.add(inputText); + fileMenu.add(outputTextboxMenu); + if(jalviewServletURL!=null) + fileMenu.add(loadApplication); + fileMenu.addSeparator(); + fileMenu.add(loadTree); + fileMenu.add(closeMenuItem); + editMenu.add(undoMenuItem); + editMenu.add(redoMenuItem); + editMenu.add(cut); + editMenu.add(copy); + editMenu.add(pasteMenu); + editMenu.add(delete); + editMenu.addSeparator(); + editMenu.add(remove2LeftMenuItem); + editMenu.add(remove2RightMenuItem); + editMenu.add(removeGappedColumnMenuItem); + editMenu.add(removeAllGapsMenuItem); + editMenu.add(removeRedundancyMenuItem); + viewMenu.add(newView); + viewMenu.addSeparator(); + viewMenu.add(menu1); + viewMenu.add(menu2); + viewMenu.addSeparator(); + viewMenu.add(annotationPanelMenuItem); + viewMenu.addSeparator(); + viewMenu.add(sequenceFeatures); + viewMenu.add(featureSettings); + viewMenu.addSeparator(); + viewMenu.add(overviewMenuItem); + colourMenu.add(applyToAllGroups); + colourMenu.addSeparator(); + colourMenu.add(noColourmenuItem); + colourMenu.add(clustalColour); + colourMenu.add(BLOSUM62Colour); + colourMenu.add(PIDColour); + colourMenu.add(zappoColour); + colourMenu.add(taylorColour); + colourMenu.add(hydrophobicityColour); + colourMenu.add(helixColour); + colourMenu.add(strandColour); + colourMenu.add(turnColour); + colourMenu.add(buriedColour); + colourMenu.add(nucleotideColour); + colourMenu.add(userDefinedColour); + colourMenu.addSeparator(); + colourMenu.add(conservationMenuItem); + colourMenu.add(modifyConservation); + colourMenu.add(abovePIDThreshold); + colourMenu.add(modifyPID); + colourMenu.add(annotationColour); + calculateMenu.add(sort); + calculateMenu.add(calculate); + calculateMenu.addSeparator(); + calculateMenu.add(pairwiseAlignmentMenuItem); + calculateMenu.add(PCAMenuItem); + calculateMenu.add(autoCalculate); + this.add(statusBar, BorderLayout.SOUTH); + pasteMenu.add(pasteNew); + pasteMenu.add(pasteThis); + sort.add(sortIDMenuItem); + sort.add(sortByTreeMenu); + sort.add(sortGroupMenuItem); + sort.add(sortPairwiseMenuItem); + calculate.add(averageDistanceTreeMenuItem); + calculate.add(neighbourTreeMenuItem); + calculate.add(avDistanceTreeBlosumMenuItem); + calculate.add(njTreeBlosumMenuItem); + helpMenu.add(documentation); + helpMenu.add(about); + menu1.add(showColumns); + menu1.add(showSeqs); + menu2.add(hideColumns); + menu2.add(hideSequences); + formatMenu.add(font); + formatMenu.add(seqLimits); + formatMenu.add(wrapMenuItem); + formatMenu.add(scaleAbove); + formatMenu.add(scaleLeft); + formatMenu.add(scaleRight); + formatMenu.add(viewBoxesMenuItem); + formatMenu.add(viewTextMenuItem); + formatMenu.add(colourTextMenuItem); + formatMenu.add(renderGapsMenuItem); + selectMenu.add(findMenuItem); + selectMenu.addSeparator(); + selectMenu.add(selectAllSequenceMenuItem); + selectMenu.add(deselectAllSequenceMenuItem); + selectMenu.add(invertSequenceMenuItem); + selectMenu.add(invertColSel); + selectMenu.add(deleteGroups); + } + + public void setEmbedded() + { + + embeddedMenu = new Panel(); + embeddedEdit = new Label("Edit"); + embeddedSelect = new Label("Select"); + embeddedView = new Label("View"); + embeddedFormat = new Label("Format"); + embeddedColour = new Label("Colour"); + embeddedFile = new Label("File"); + embeddedHelp = new Label("Help"); + embeddedCalculate = new Label("Calculate"); + flowLayout1 = new FlowLayout(); + embeddedMenu.setBackground(Color.lightGray); + embeddedMenu.setLayout(flowLayout1); + embeddedEdit.setFont(new java.awt.Font("Arial", Font.PLAIN, 10)); + embeddedSelect.setFont(new java.awt.Font("Arial", Font.PLAIN, 10)); + embeddedView.setFont(new java.awt.Font("Arial", Font.PLAIN, 10)); + embeddedFormat.setFont(new java.awt.Font("Arial", Font.PLAIN, 10)); + embeddedColour.setFont(new java.awt.Font("Arial", Font.PLAIN, 10)); + embeddedFile.setFont(new java.awt.Font("Arial", Font.PLAIN, 10)); + embeddedHelp.setFont(new java.awt.Font("Arial", Font.PLAIN, 10)); + embeddedCalculate.setFont(new java.awt.Font("Arial", Font.PLAIN, 10)); + embeddedMenu.add(embeddedFile); + embeddedMenu.add(embeddedEdit); + embeddedMenu.add(embeddedSelect); + embeddedMenu.add(embeddedView); + embeddedMenu.add(embeddedFormat); + embeddedMenu.add(embeddedColour); + embeddedMenu.add(embeddedCalculate); + embeddedMenu.add(embeddedHelp); + flowLayout1.setAlignment(FlowLayout.LEFT); + flowLayout1.setHgap(2); + flowLayout1.setVgap(0); + embeddedFile.addMouseListener(this); + embeddedEdit.addMouseListener(this); + embeddedSelect.addMouseListener(this); + embeddedView.addMouseListener(this); + embeddedFormat.addMouseListener(this); + embeddedColour.addMouseListener(this); + embeddedCalculate.addMouseListener(this); + embeddedHelp.addMouseListener(this); + + // setVisible(false); + fileMenu.remove(closeMenuItem); + fileMenu.remove(3); // Seperator + + viewport.applet.setLayout(new BorderLayout()); + viewport.applet.add(embeddedMenu, BorderLayout.NORTH); + viewport.applet.add(statusBar, BorderLayout.SOUTH); + // viewport.applet.validate(); + + alignPanel.setSize(viewport.applet.size().width, viewport.applet.size().height + - embeddedMenu.HEIGHT - statusBar.HEIGHT); + + viewport.applet.add(alignPanel, BorderLayout.CENTER); + viewport.applet.validate(); + + } + + + + PopupMenu filePopup, editPopup, searchPopup, + viewPopup, formatPopup, colourPopup, calculatePopup, helpPopup; + MenuItem featureSettings = new MenuItem(); + CheckboxMenuItem sequenceFeatures = new CheckboxMenuItem(); + MenuItem annotationColour = new MenuItem(); + MenuItem invertColSel = new MenuItem(); + Menu menu1 = new Menu(); + MenuItem showColumns = new MenuItem(); + MenuItem showSeqs = new MenuItem(); + Menu menu2 = new Menu(); + MenuItem hideColumns = new MenuItem(); + MenuItem hideSequences = new MenuItem(); + Menu formatMenu = new Menu(); + Menu selectMenu = new Menu(); + MenuItem newView = new MenuItem(); + + public void mousePressed(MouseEvent evt) + { + PopupMenu popup = null; + Label source = (Label)evt.getSource(); + if(source==embeddedFile) + { + popup = filePopup = genPopupMenu(filePopup, fileMenu); + } + else if(source==embeddedEdit) + { + popup = editPopup = genPopupMenu(editPopup, editMenu); + } + else if(source==embeddedSelect) + { + popup = searchPopup = genPopupMenu(searchPopup, selectMenu); + } + else if(source==embeddedView) + { + popup = viewPopup = genPopupMenu(viewPopup, viewMenu); + } + else if (source ==embeddedFormat) + { + popup = formatPopup = genPopupMenu(formatPopup, formatMenu); + } + else if(source==embeddedColour) + { + popup = colourPopup = genPopupMenu(colourPopup, colourMenu); + } + else if(source==embeddedCalculate) + { + popup = calculatePopup = genPopupMenu(calculatePopup, calculateMenu); + } + else if(source==embeddedHelp) + { + popup = helpPopup = genPopupMenu(helpPopup, helpMenu); + } + + embeddedMenu.add(popup); + popup.show(embeddedMenu, + source.getBounds().x, + source.getBounds().y + source.getBounds().getSize().height); + } + + PopupMenu genPopupMenu(PopupMenu popup, Menu original) + { + if(popup!=null) + { + return popup; + } + popup = new PopupMenu(); + int m, mSize = original.getItemCount(); + for(m=0; m