X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FAlignFrame.java;h=4ee6e27390379e29054637fe6b614cb06fd51109;hb=6366cf9dcc083ef36aa9fe822bf49fbc18100dca;hp=fae50d9e45073d08a22f98813773b311637f8fdb;hpb=c80c766368e646a58a8e467cfdd2785a635f7fed;p=jalview.git diff --git a/src/jalview/appletgui/AlignFrame.java b/src/jalview/appletgui/AlignFrame.java index fae50d9..4ee6e27 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) 2007 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 @@ -19,127 +19,1001 @@ package jalview.appletgui; -import jalview.jbappletgui.GAlignFrame; -import jalview.schemes.*; -import jalview.datamodel.*; -import jalview.analysis.*; -import jalview.io.*; +import java.io.*; +import java.net.*; +import java.util.*; + import java.awt.*; import java.awt.event.*; -import java.util.*; -import java.io.InputStreamReader; -import java.io.BufferedReader; -public class AlignFrame - extends GAlignFrame -{ - 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; +import jalview.analysis.*; +import jalview.commands.*; +import jalview.datamodel.*; +import jalview.io.*; +import jalview.schemes.*; + +public class AlignFrame + extends Frame implements ActionListener, + ItemListener, KeyListener, MouseListener +{ + public AlignmentPanel alignPanel; + public AlignViewport viewport; + int DEFAULT_WIDTH = 700; + int DEFAULT_HEIGHT = 500; + + String jalviewServletURL; + + public AlignFrame(AlignmentI al, + jalview.bin.JalviewLite applet, + String title, + boolean embedded) + { + + if (applet != null) + { + jalviewServletURL = applet.getParameter("APPLICATION_URL"); + } + + try + { + jbInit(); + } + catch (Exception ex) + { + ex.printStackTrace(); + } + + viewport = new AlignViewport(al, applet); + alignPanel = new AlignmentPanel(this, viewport); + + viewport.updateConservation(alignPanel); + viewport.updateConsensus(alignPanel); + + annotationPanelMenuItem.setState(viewport.showAnnotation); + + seqLimits.setState(viewport.showJVSuffix); + + if (applet != null) + { + String param = applet.getParameter("sortBy"); + if (param != null) + { + if (param.equalsIgnoreCase("Id")) + { + sortIDMenuItem_actionPerformed(); + } + else if (param.equalsIgnoreCase("Pairwise Identity")) + { + sortPairwiseMenuItem_actionPerformed(); + } + } + + param = applet.getParameter("wrap"); + if (param != null) + { + if (param.equalsIgnoreCase("true")) + { + wrapMenuItem.setState(true); + wrapMenuItem_actionPerformed(); + } + } + + try + { + 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.paintAlignment(true); + } + + public AlignViewport getAlignViewport() + { + return viewport; + } + + public SeqCanvas getSeqcanvas() + { + 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.paintAlignment(true); + } + + } + + public void keyPressed(KeyEvent evt) + { + if (viewport.cursorMode && + ( (evt.getKeyCode() >= KeyEvent.VK_0 && + evt.getKeyCode() <= KeyEvent.VK_9) + || + (evt.getKeyCode() >= KeyEvent.VK_NUMPAD0 && + evt.getKeyCode() <= KeyEvent.VK_NUMPAD9) + ) + && Character.isDigit(evt.getKeyChar())) + 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 (evt.isAltDown() || !viewport.cursorMode) + slideSequences(false, + alignPanel.seqPanel.getKeyboardNo1()); + else + alignPanel.seqPanel.moveCursor( -1, 0); + break; + + case KeyEvent.VK_RIGHT: + if (evt.isAltDown() || !viewport.cursorMode) + slideSequences(true, + alignPanel.seqPanel.getKeyboardNo1()); + else + 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() != 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.paintAlignment(true); + } + + 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.paintAlignment(true); + } + + 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 == loadAnnotations) + { + loadAnnotations(); + } + else if (source == outputAnnotations) + { + outputAnnotations(true); + } + else if (source == outputFeatures) + { + outputFeatures(true, "Jalview"); + } + 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.paintAlignment(true); + } + 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.paintAlignment(true); + } + else if (source == showSeqs) + { + viewport.showAllHiddenSeqs(); + } + else if (source == hideColumns) + { + viewport.hideSelectedColumns(); + alignPanel.paintAlignment(true); + } + 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 AlignFrame(AlignmentI al) + public void inputText_actionPerformed() { - this.applet = null; - viewport = new AlignViewport(al, null); - alignPanel = new AlignmentPanel(this, viewport); - add(alignPanel); - alignPanel.validate(); + CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this); + Frame frame = new Frame(); + frame.add(cap); + jalview.bin.JalviewLite.addFrame(frame, "Cut & Paste Input", 500, 500); + } + + protected void outputText_actionPerformed(ActionEvent e) + { + 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(new AppletFormatAdapter().formatSequences(e.getActionCommand(), + viewport.getAlignment(), + viewport.showJVSuffix)); + } + + public void loadAnnotations() + { + CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this); + cap.setText("Paste your features / annotations file here."); + cap.setAnnotationImport(); + Frame frame = new Frame(); + frame.add(cap); + jalview.bin.JalviewLite.addFrame(frame, "Paste Annotations ", 400, 300); + + } + + public String outputAnnotations(boolean displayTextbox) + { + String annotation = new AnnotationFile().printAnnotations( + viewport.showAnnotation ? viewport.alignment.getAlignmentAnnotation() : null, + viewport.alignment.getGroups()); - this.addWindowListener(new WindowAdapter() + if (displayTextbox) { - public void windowClosing(WindowEvent e) - { - closeMenuItem_actionPerformed(null); - } - }); + CutAndPasteTransfer cap = new CutAndPasteTransfer(false, this); + Frame frame = new Frame(); + frame.add(cap); + jalview.bin.JalviewLite.addFrame(frame, + "Annotations", + 600, 500); + cap.setText(annotation); + } + return annotation; } + public String outputFeatures(boolean displayTextbox, String format) + { + String features; + if (format.equalsIgnoreCase("Jalview")) + { + features = new FeaturesFile().printJalviewFormat( + viewport.alignment.getSequencesArray(), + viewport.featuresDisplayed); + } + else + { + features = new FeaturesFile().printGFFFormat( + viewport.alignment.getSequencesArray(), + viewport.featuresDisplayed); + } + + if (displayTextbox) + { + CutAndPasteTransfer cap = new CutAndPasteTransfer(false, this); + Frame frame = new Frame(); + frame.add(cap); + jalview.bin.JalviewLite.addFrame(frame, + "Features", + 600, 500); + + cap.setText(features); + } + + return features; + } - public AlignFrame(AlignmentI al, jalview.bin.JalviewLite applet) + void launchFullApplication() { - this.applet = applet; - viewport = new AlignViewport(al, applet); - alignPanel = new AlignmentPanel(this, viewport); - add(alignPanel); - alignPanel.validate(); + StringBuffer url = new StringBuffer(jalviewServletURL); + + url.append("?open=" + + appendProtocol(viewport.applet.getParameter("file"))); - String treeFile = applet.getParameter("treeFile"); - if (treeFile != null) + if (viewport.applet.getParameter("features") != null) { - try - { - treeFile = treeFile; - jalview.io.NewickFile fin = new jalview.io.NewickFile(applet. - getCodeBase() + treeFile, "URL"); - fin.parse(); + url.append("&features="); + url.append(appendProtocol(viewport.applet.getParameter("features"))); + } - if (fin.getTree() != null) - { - 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); - } - } - catch (Exception ex) - { - ex.printStackTrace(); - } + if (viewport.applet.getParameter("annotations") != null) + { + url.append("&annotations="); + url.append(appendProtocol(viewport.applet.getParameter("annotations"))); } - this.addWindowListener(new WindowAdapter() + if (viewport.applet.getParameter("jnetfile") != null) { - public void windowClosing(WindowEvent e) - { - closeMenuItem_actionPerformed(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"); } - public void inputText_actionPerformed(ActionEvent e) + String removeWhiteSpace(String colour) { - CutAndPasteTransfer cap = new CutAndPasteTransfer(true); - Frame frame = new Frame(); - frame.add(cap); - jalview.bin.JalviewLite.addFrame(frame, "Cut & Paste Input", 500, 500); + 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(); } - protected void outputText_actionPerformed(ActionEvent e) + String appendProtocol(String url) { - CutAndPasteTransfer cap = new CutAndPasteTransfer(false); - 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())); + 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() { - PaintRefresher.components.remove(viewport.alignment); - 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); + } - Stack historyList = new Stack(); - Stack redoList = new Stack(); + this.dispose(); + } + /** + * 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 { @@ -147,11 +1021,12 @@ 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 { @@ -160,74 +1035,104 @@ 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; + } - protected void redoMenuItem_actionPerformed(ActionEvent e) - { - HistoryItem hi = (HistoryItem) redoList.pop(); - restoreHistoryItem(hi); + CommandI command = (CommandI) viewport.historyList.pop(); + viewport.redoList.push(command); + command.undoCommand(); + + AlignViewport originalSource = getOriginatingSource(command); + + originalSource.hasHiddenColumns = viewport.colSel.getHiddenColumns() != null; updateEditMenuBar(); - viewport.updateConsensus(); - alignPanel.repaint(); - alignPanel.repaint(); + originalSource.firePropertyChange("alignment", null, + originalSource.alignment.getSequences()); } - // used by undo and redo - void restoreHistoryItem(HistoryItem hi) + /** + * DOCUMENT ME! + * + * @param e DOCUMENT ME! + */ + protected void redoMenuItem_actionPerformed() { - if (hi.getType() == HistoryItem.SORT) + if (viewport.redoList.size() < 1) { - for (int i = 0; i < hi.getSequences().size(); i++) - { - viewport.alignment.getSequences().setElementAt(hi.getSequences(). - elementAt(i), i); - } + return; } - else + + CommandI command = (CommandI) viewport.redoList.pop(); + viewport.historyList.push(command); + command.doCommand(); + + AlignViewport originalSource = getOriginatingSource(command); + originalSource.hasHiddenColumns = viewport.colSel.getHiddenColumns() != null; + + updateEditMenuBar(); + originalSource.firePropertyChange("alignment", null, + originalSource.alignment.getSequences()); + } + + AlignViewport getOriginatingSource(CommandI command) + { + 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++) { - 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 (al == ( (AlignmentPanel) comps.elementAt(i)).av.alignment) + { + originalSource = ( (AlignmentPanel) comps.elementAt(i)).av; + break; + } } } - if (hi.getType() == HistoryItem.PASTE) + } + + if (originalSource == null) + { + //The original view is closed, we must validate + //the current view against the closed view first + if (al != null) { - for (int i = viewport.alignment.getHeight() - 1; - i > hi.getSequences().size() - 1; i--) - { - viewport.alignment.deleteSequence(i); - } + PaintRefresher.validateSequences(al, viewport.alignment); } - } - updateEditMenuBar(); + originalSource = viewport; + } - viewport.updateConsensus(); - viewport.updateConservation(); - alignPanel.repaint(); + return originalSource; } public void moveSelectedSequences(boolean up) @@ -243,13 +1148,13 @@ 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(null).contains(seq)) { continue; } SequenceI temp = viewport.alignment.getSequenceAt(i - 1); - if (sg.sequences.contains(temp)) + if (sg.getSequences(null).contains(temp)) { continue; } @@ -263,13 +1168,13 @@ 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(viewport.hiddenRepSequences).contains(seq)) { continue; } SequenceI temp = viewport.alignment.getSequenceAt(i + 1); - if (sg.sequences.contains(temp)) + if (sg.getSequences(viewport.hiddenRepSequences).contains(temp)) { continue; } @@ -279,11 +1184,101 @@ public class AlignFrame } } - alignPanel.repaint(); + alignPanel.paintAlignment(true); + } + + synchronized void slideSequences(boolean right, int size) + { + Vector sg = new Vector(); + if(viewport.cursorMode) + { + sg.addElement(viewport.alignment.getSequenceAt( + alignPanel.seqPanel.seqCanvas.cursorY)); + } + else if(viewport.getSelectionGroup()!=null + && viewport.getSelectionGroup().getSize()!=viewport.alignment.getHeight()) + { + sg = viewport.getSelectionGroup().getSequences( + viewport.hiddenRepSequences); + } + + if(sg.size()<1) + { + return; + } + + Vector invertGroup = new Vector(); + + for (int i = 0; i < viewport.alignment.getHeight(); i++) + { + if(!sg.contains(viewport.alignment.getSequenceAt(i))) + invertGroup.addElement(viewport.alignment.getSequenceAt(i)); + } + + SequenceI[] seqs1 = new SequenceI[sg.size()]; + for (int i = 0; i < sg.size(); i++) + seqs1[i] = (SequenceI) sg.elementAt(i); + + SequenceI[] seqs2 = new SequenceI[invertGroup.size()]; + for (int i = 0; i < invertGroup.size(); i++) + seqs2[i] = (SequenceI) invertGroup.elementAt(i); + + SlideSequencesCommand ssc; + if (right) + ssc = new SlideSequencesCommand("Slide Sequences", + seqs2, seqs1, size, + viewport.getGapCharacter() + ); + else + ssc = new SlideSequencesCommand("Slide Sequences", + seqs1, seqs2, size, + viewport.getGapCharacter() + ); + + int groupAdjustment = 0; + if (ssc.getGapsInsertedBegin() && right) + { + if (viewport.cursorMode) + alignPanel.seqPanel.moveCursor(size, 0); + else + groupAdjustment = size; + } + else if (!ssc.getGapsInsertedBegin() && !right) + { + if (viewport.cursorMode) + alignPanel.seqPanel.moveCursor( -size, 0); + else + groupAdjustment = -size; + } + + if (groupAdjustment != 0) + { + viewport.getSelectionGroup().setStartRes( + viewport.getSelectionGroup().getStartRes() + groupAdjustment); + viewport.getSelectionGroup().setEndRes( + viewport.getSelectionGroup().getEndRes() + groupAdjustment); + } + + + boolean appendHistoryItem = false; + if(viewport.historyList!=null + && viewport.historyList.size()>0 + && viewport.historyList.peek() instanceof SlideSequencesCommand) + { + appendHistoryItem = ssc.appendSlideCommand( + (SlideSequencesCommand)viewport.historyList.peek()) + ; + } + + if(!appendHistoryItem) + addHistoryItem(ssc); + + repaint(); } - StringBuffer copiedSequences; - protected void copy_actionPerformed(ActionEvent e) + static StringBuffer copiedSequences; + static Vector copiedHiddenColumns; + protected void copy_actionPerformed() { if (viewport.getSelectionGroup() == null) { @@ -303,65 +1298,83 @@ public class AlignFrame int index = 0, startRes, endRes; char ch; + if (viewport.hasHiddenColumns && viewport.getSelectionGroup() != null) + { + copiedHiddenColumns = new Vector(); + int hiddenOffset = viewport.getSelectionGroup().getStartRes(); + for (int i = 0; i < viewport.getColumnSelection().getHiddenColumns().size(); + i++) + { + 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(); i++) { - SequenceI seq = null; + SequenceI seq = null; - while (seq == null) + while (seq == null) + { + if (orderedSeqs.containsKey(index + "")) { - if (orderedSeqs.containsKey(index + "")) - { - seq = (SequenceI) orderedSeqs.get(index + ""); - index++; + seq = (SequenceI) orderedSeqs.get(index + ""); + index++; - break; - } - else - { - index++; - } + break; } + else + { + index++; + } + } - //FIND START RES - //Returns residue following index if gap - startRes = seq.findPosition(sg.getStartRes()); + //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; + //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++) + for (int j = 0; j < sg.getEndRes() + 1 && j < seq.getLength(); j++) + { + ch = seq.getCharAt(j); + if (!jalview.util.Comparison.isGap( (ch))) { - ch = seq.getCharAt(j); - if (!jalview.util.Comparison.isGap( (ch))) - { - endRes++; - } + endRes++; } + } - if(endRes>0) - { - endRes += seq.getStart() -1; - } + if (endRes > 0) + { + endRes += seq.getStart() - 1; + } - copiedSequences.append(seq.getName() + "\t" + - startRes + "\t" + - endRes + "\t" + - seq.getSequence(sg.getStartRes(), - sg.getEndRes() + 1) + "\n"); + copiedSequences.append(seq.getName() + "\t" + + startRes + "\t" + + endRes + "\t" + + seq.getSequenceAsString(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); } @@ -369,6 +1382,7 @@ public class AlignFrame { try { + if (copiedSequences == null) { return; @@ -381,27 +1395,16 @@ 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")) { @@ -411,16 +1414,25 @@ 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 { - viewport.setEndSeq(viewport.alignment.getHeight()); - viewport.alignment.getWidth(); - viewport.updateConservation(); - viewport.updateConsensus(); - alignPanel.repaint(); + addSequences(newSeqs); } } @@ -429,99 +1441,127 @@ public class AlignFrame } - protected void cut_actionPerformed(ActionEvent e) + void addSequences(SequenceI[] seqs) { - copy_actionPerformed(null); - delete_actionPerformed(null); + for (int i = 0; i < seqs.length; i++) + { + viewport.alignment.addSequence(seqs[i]); + } + + //!newAlignment + addHistoryItem(new EditCommand( + "Add sequences", + EditCommand.PASTE, + seqs, + 0, + viewport.alignment.getWidth(), + viewport.alignment) + ); + + viewport.setEndSeq(viewport.alignment.getHeight()); + viewport.alignment.getWidth(); + viewport.firePropertyChange("alignment", null, + viewport.alignment.getSequences()); + } - protected void delete_actionPerformed(ActionEvent e) + protected void cut_actionPerformed() { - addHistoryItem(new HistoryItem("Delete Sequences", viewport.alignment, - HistoryItem.HIDE)); - if (viewport.getSelectionGroup() == null) - { - return; - } + copy_actionPerformed(); + delete_actionPerformed(); + } + protected void delete_actionPerformed() + { SequenceGroup sg = viewport.getSelectionGroup(); - boolean allSequences = false; - if(sg.sequences.size()==viewport.alignment.getHeight()) - allSequences = true; - - for (int i = 0; i < sg.sequences.size(); i++) + if (sg == null) { - SequenceI seq = sg.getSequenceAt(i); - int index = viewport.getAlignment().findIndex(seq); - seq.deleteChars(sg.getStartRes(), sg.getEndRes() + 1); - - // If the cut affects all sequences, remove highlighted columns - if (allSequences) - { - viewport.getColumnSelection().removeElements(sg.getStartRes(), - sg.getEndRes() + 1); - } + return; + } + Vector seqs = new Vector(); + SequenceI seq; + for (int i = 0; i < sg.getSize(); i++) + { + seq = sg.getSequenceAt(i); + seqs.addElement(seq); + } - if (seq.getSequence().length() < 1) - { - viewport.getAlignment().deleteSequence(seq); - } - else - { - viewport.getAlignment().getSequences().setElementAt(seq, index); - } + // If the cut affects all sequences, remove highlighted columns + if (sg.getSize() == viewport.alignment.getHeight()) + { + viewport.getColumnSelection().removeElements(sg.getStartRes(), + sg.getEndRes() + 1); + } + + SequenceI[] cut = new SequenceI[seqs.size()]; + for (int i = 0; i < seqs.size(); i++) + { + cut[i] = (SequenceI) seqs.elementAt(i); } + /* + //ADD HISTORY ITEM + */ + addHistoryItem(new EditCommand("Cut Sequences", + EditCommand.CUT, + cut, + sg.getStartRes(), + sg.getEndRes() - sg.getStartRes() + 1, + viewport.alignment)); + viewport.setSelectionGroup(null); viewport.alignment.deleteGroup(sg); - viewport.resetSeqLimits(alignPanel.seqPanel.seqCanvas.getSize().height); + + viewport.firePropertyChange("alignment", null, + viewport.getAlignment().getSequences()); + if (viewport.getAlignment().getHeight() < 1) { - try - { - this.setVisible(false); - } - catch (Exception ex) - {} + this.setVisible(false); } - viewport.updateConservation(); - viewport.updateConsensus(); - alignPanel.repaint(); - } - protected void deleteGroups_actionPerformed(ActionEvent e) + protected void deleteGroups_actionPerformed() { viewport.alignment.deleteAllGroups(); + viewport.sequenceColours = null; viewport.setSelectionGroup(null); - alignPanel.repaint(); + alignPanel.paintAlignment(true); } - public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e) + public void selectAllSequenceMenuItem_actionPerformed() { SequenceGroup sg = new SequenceGroup(); for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++) { sg.addSequence(viewport.getAlignment().getSequenceAt(i), false); } - sg.setEndRes(viewport.alignment.getWidth()-1); + sg.setEndRes(viewport.alignment.getWidth() - 1); viewport.setSelectionGroup(sg); - alignPanel.repaint(); - PaintRefresher.Refresh(null, viewport.alignment); + alignPanel.paintAlignment(true); + PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId()); } - public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e) + public void deselectAllSequenceMenuItem_actionPerformed() { + if (viewport.cursorMode) + { + alignPanel.seqPanel.keyboardNo1 = null; + alignPanel.seqPanel.keyboardNo2 = null; + } viewport.setSelectionGroup(null); viewport.getColumnSelection().clear(); viewport.setSelectionGroup(null); - PaintRefresher.Refresh(null, viewport.alignment); + alignPanel.idPanel.idCanvas.searchResults = null; + alignPanel.seqPanel.seqCanvas.highlightSearchResults(null); + alignPanel.paintAlignment(true); + PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId()); } - public void invertSequenceMenuItem_actionPerformed(ActionEvent e) + public void invertSequenceMenuItem_actionPerformed() { SequenceGroup sg = viewport.getSelectionGroup(); for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++) @@ -529,212 +1569,253 @@ public class AlignFrame sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false); } - PaintRefresher.Refresh(null, viewport.alignment); + PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId()); } - public void remove2LeftMenuItem_actionPerformed(ActionEvent e) + void trimAlignment(boolean trimLeft) { ColumnSelection colSel = viewport.getColumnSelection(); + int column; + if (colSel.size() > 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) { - viewport.getSelectionGroup().adjustForRemoveLeft(min); + seqs = viewport.getSelectionGroup().getSequencesAsArray(viewport. + hiddenRepSequences); } - - Vector groups = viewport.alignment.getGroups(); - for (int i = 0; i < groups.size(); i++) + else { - SequenceGroup sg = (SequenceGroup) groups.elementAt(i); - if (!sg.adjustForRemoveLeft(min)) - { - viewport.alignment.deleteGroup(sg); - } + seqs = viewport.alignment.getSequencesArray(); } - alignPanel.repaint(); - } - } - - 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) + TrimRegionCommand trimRegion; + if (trimLeft) + { + trimRegion = new TrimRegionCommand("Remove Left", + TrimRegionCommand.TRIM_LEFT, + seqs, + column, + viewport.alignment, + viewport.colSel, + viewport.selectionGroup); + viewport.setStartRes(0); + } + else { - viewport.getSelectionGroup().adjustForRemoveRight(max); + 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.adjustForRemoveRight(max)) + + if ( (trimLeft && !sg.adjustForRemoveLeft(column)) + || (!trimLeft && !sg.adjustForRemoveRight(column))) { viewport.alignment.deleteGroup(sg); } } - alignPanel.repaint(); + viewport.firePropertyChange("alignment", null, + viewport.getAlignment().getSequences()); } - } - public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e) + public void removeGappedColumnMenuItem_actionPerformed() { - addHistoryItem(new HistoryItem("Remove Gapped Columns", - viewport.alignment, - HistoryItem.HIDE)); - viewport.getAlignment().removeGaps(); - viewport.updateConservation(); - viewport.updateConsensus(); - alignPanel.repaint(); - } + int start = 0, end = viewport.alignment.getWidth() - 1; - public void removeAllGapsMenuItem_actionPerformed(ActionEvent e) - { - addHistoryItem(new HistoryItem("Remove Gaps", viewport.alignment, - HistoryItem.HIDE)); + SequenceI[] seqs; + if (viewport.getSelectionGroup() != null) + { + seqs = viewport.getSelectionGroup().getSequencesAsArray(viewport. + hiddenRepSequences); + start = viewport.getSelectionGroup().getStartRes(); + end = viewport.getSelectionGroup().getEndRes(); + } + else + { + seqs = viewport.alignment.getSequencesArray(); + } - SequenceI current; - int jSize; + RemoveGapColCommand removeGapCols = + new RemoveGapColCommand("Remove Gapped Columns", + seqs, + start, end, + viewport.alignment); - Vector seqs=null; + addHistoryItem(removeGapCols); - int start=0, end = viewport.alignment.getWidth(); + statusBar.setText("Removed " + removeGapCols.getSize() + " empty columns."); - if (viewport.getSelectionGroup() != null - && viewport.getSelectionGroup().sequences != null - && viewport.getSelectionGroup().sequences.size()>0) + //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() + { + int start = 0, end = viewport.alignment.getWidth() - 1; + + SequenceI[] seqs; + if (viewport.getSelectionGroup() != null) { - seqs = viewport.getSelectionGroup().sequences; + seqs = viewport.getSelectionGroup().getSequencesAsArray(viewport. + hiddenRepSequences); start = viewport.getSelectionGroup().getStartRes(); end = viewport.getSelectionGroup().getEndRes(); } else - seqs = viewport.alignment.getSequences(); + { + 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.alignment)); - for (int i = 0; i -1) + { + title = title.substring(0, title.indexOf("(View")); + } - public void findMenuItem_actionPerformed(ActionEvent e) - { - Finder finder = new Finder(alignPanel); - } + title += "(View " + viewSize + ")"; - public void font_actionPerformed(ActionEvent e) - { - Frame frame = new Frame(); - FontChooser fc = new FontChooser(alignPanel, frame); - frame.add(fc); - jalview.bin.JalviewLite.addFrame(frame, "Change Font", 440, 100); + newaf.setTitle(title.toString()); + + newaf.viewport.historyList = viewport.historyList; + newaf.viewport.redoList = viewport.redoList; } - protected void fullSeqId_actionPerformed(ActionEvent e) + public void seqLimits_itemStateChanged() { - viewport.setShowFullId(fullSeqId.getState()); + viewport.setShowJVSuffix(seqLimits.getState()); alignPanel.fontChanged(); - alignPanel.repaint(); + alignPanel.paintAlignment(true); } - protected void colourTextMenuItem_actionPerformed(ActionEvent e) + protected void colourTextMenuItem_actionPerformed() { viewport.setColourText(colourTextMenuItem.getState()); - alignPanel.repaint(); + alignPanel.paintAlignment(true); } - protected void wrapMenuItem_actionPerformed(ActionEvent e) + protected void wrapMenuItem_actionPerformed() { viewport.setWrapAlignment(wrapMenuItem.getState()); alignPanel.setWrapAlignment(wrapMenuItem.getState()); scaleAbove.setEnabled(wrapMenuItem.getState()); scaleLeft.setEnabled(wrapMenuItem.getState()); scaleRight.setEnabled(wrapMenuItem.getState()); - 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()); + alignPanel.paintAlignment(true); } - public void overviewMenuItem_actionPerformed(ActionEvent e) + public void overviewMenuItem_actionPerformed() { if (alignPanel.overviewPanel != null) { @@ -746,8 +1827,8 @@ public class AlignFrame frame.add(overview); // +50 must allow for applet frame window jalview.bin.JalviewLite.addFrame(frame, "Overview " + this.getTitle(), - overview.preferredSize().width, - overview.preferredSize().height + 50); + overview.getPreferredSize().width, + overview.getPreferredSize().height + 50); frame.pack(); frame.addWindowListener(new WindowAdapter() @@ -762,68 +1843,11 @@ 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(cs!=null) + if (cs != null) { if (viewport.getAbovePIDThreshold()) { @@ -861,7 +1885,7 @@ public class AlignFrame cs.setConservation(null); } - cs.setConsensus(viewport.vconsensus); + cs.setConsensus(viewport.hconsensus); } viewport.setGlobalColourScheme(cs); @@ -873,14 +1897,16 @@ public class AlignFrame { SequenceGroup sg = (SequenceGroup) groups.elementAt(i); - if(cs==null) + 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(viewport.hiddenRepSequences), + sg.getWidth()); } else { @@ -900,16 +1926,20 @@ public class AlignFrame || cs instanceof Blosum62ColourScheme) { sg.cs.setThreshold(threshold, viewport.getIgnoreGapsConsensus()); - sg.cs.setConsensus(AAFrequency.calculate(sg.sequences, 0, sg.getWidth())); + sg.cs.setConsensus(AAFrequency.calculate( + sg.getSequences(viewport.hiddenRepSequences), 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(viewport. + hiddenRepSequences), 0, viewport.alignment.getWidth() - 1); c.calculate(); c.verdict(false, viewport.ConsPercGaps); @@ -924,20 +1954,20 @@ public class AlignFrame } } - if (alignPanel.getOverviewPanel() != null) { alignPanel.getOverviewPanel().updateOverviewImage(); } - alignPanel.repaint(); - } - + jalview.structure.StructureSelectionManager.getStructureSelectionManager() + .sequenceColoursChanged(alignPanel); + alignPanel.paintAlignment(true); + } - protected void modifyPID_actionPerformed(ActionEvent e) + protected void modifyPID_actionPerformed() { - if (viewport.getAbovePIDThreshold() && viewport.globalColourScheme!=null) + if (viewport.getAbovePIDThreshold() && viewport.globalColourScheme != null) { SliderPanel.setPIDSliderSource(alignPanel, viewport.getGlobalColourScheme(), "Background"); @@ -945,9 +1975,9 @@ public class AlignFrame } } - protected void modifyConservation_actionPerformed(ActionEvent e) + protected void modifyConservation_actionPerformed() { - if (viewport.getConservationSelected() && viewport.globalColourScheme!=null) + if (viewport.getConservationSelected() && viewport.globalColourScheme != null) { SliderPanel.setConservationSlider(alignPanel, viewport.globalColourScheme, "Background"); @@ -955,7 +1985,7 @@ public class AlignFrame } } - protected void conservationMenuItem_actionPerformed(ActionEvent e) + protected void conservationMenuItem_actionPerformed() { viewport.setConservationSelected(conservationMenuItem.getState()); @@ -964,10 +1994,10 @@ public class AlignFrame changeColour(viewport.getGlobalColourScheme()); - modifyConservation_actionPerformed(null); + modifyConservation_actionPerformed(); } - public void abovePIDThreshold_actionPerformed(ActionEvent e) + public void abovePIDThreshold_actionPerformed() { viewport.setAbovePIDThreshold(abovePIDThreshold.getState()); @@ -976,72 +2006,72 @@ public class AlignFrame changeColour(viewport.getGlobalColourScheme()); - modifyPID_actionPerformed(null); - } - - public void userDefinedColour_actionPerformed(ActionEvent e) - { - UserDefinedColours chooser = new UserDefinedColours(alignPanel, null); - } - - public void PIDColour_actionPerformed(ActionEvent e) - { - changeColour(new PIDColourScheme()); - } - - public void BLOSUM62Colour_actionPerformed(ActionEvent e) - { - changeColour(new Blosum62ColourScheme()); + modifyPID_actionPerformed(); } - 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)); - alignPanel.repaint(); + addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder, + viewport.alignment)); + alignPanel.paintAlignment(true); } - 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(); + alignPanel.paintAlignment(true); } - 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()); - alignPanel.repaint(); + alignPanel.paintAlignment(true); } - 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() > 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.paintAlignment(true); + } if ( (viewport.getSelectionGroup() != null && viewport.getSelectionGroup().getSize() < 4 && @@ -1053,11 +2083,7 @@ 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) { @@ -1065,24 +2091,24 @@ 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"); + NewTreePanel("AV", "BL", "Average distance tree using BLOSUM62"); } void NewTreePanel(String type, String pwType, String title) @@ -1103,27 +2129,43 @@ public class AlignFrame current.insertCharAt(Width - 1, viewport.getGapCharacter()); } } - alignPanel.repaint(); + alignPanel.paintAlignment(true); } - 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() > 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.setTreeImport(); + 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) @@ -1132,12 +2174,12 @@ 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(); + alignPanel.paintAlignment(true); } }); @@ -1150,19 +2192,22 @@ public class AlignFrame }); } - protected void documentation_actionPerformed(ActionEvent e) + protected void documentation_actionPerformed() { - jalview.bin.JalviewLite.showURL("http://www.jalview.org/help.html"); + 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; } + { + this.version = version; + } public void paint(Graphics g) { @@ -1174,7 +2219,7 @@ public class AlignFrame int y = 5, x = 7; g.setColor(Color.black); g.setFont(new Font("Helvetica", Font.BOLD, 14)); - g.drawString("Jalview - Release "+version, 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); @@ -1186,7 +2231,7 @@ 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); } } @@ -1213,10 +2258,587 @@ public class AlignFrame } } - Frame frame = new Frame(); 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 loadAnnotations = new MenuItem( + "Load Features/Annotations ..."); + protected MenuItem outputFeatures = new MenuItem("Export Features ..."); + protected MenuItem outputAnnotations = new MenuItem("Export Annotations ..."); + + 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); + loadAnnotations.addActionListener(this); + outputFeatures.addActionListener(this); + outputAnnotations.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); + 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(loadTree); + fileMenu.add(loadAnnotations); + + fileMenu.addSeparator(); + fileMenu.add(outputTextboxMenu); + fileMenu.add(outputFeatures); + fileMenu.add(outputAnnotations); + + if (jalviewServletURL != null) + { + fileMenu.add(loadApplication); + } + + fileMenu.addSeparator(); + 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); + + fileMenu.remove(closeMenuItem); + fileMenu.remove(3); // Seperator + + viewport.applet.setLayout(new BorderLayout()); + viewport.applet.add(embeddedMenu, BorderLayout.NORTH); + viewport.applet.add(statusBar, BorderLayout.SOUTH); + + alignPanel.setSize(viewport.applet.getSize().width, + viewport.applet.getSize().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 < mSize; m++) + { + popup.add(original.getItem(m)); + mSize--; + m--; + } + + return popup; + } + + public void mouseClicked(MouseEvent evt) + {} + + public void mouseReleased(MouseEvent evt) + {} + + public void mouseEntered(MouseEvent evt) + {} + + public void mouseExited(MouseEvent evt) + {} + }