X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FAlignFrame.java;h=9ba6cca8306535f98ca02cefd7af2f2c36c8f67c;hb=419c2468cfaadbb42a96d483415fd657e7174f94;hp=1cfddf8bc5eb3bf54c7ee68fc9fcc4fbacf5c655;hpb=89407753e8e178e700a0fa6d955db5663d80c10c;p=jalview.git diff --git a/src/jalview/appletgui/AlignFrame.java b/src/jalview/appletgui/AlignFrame.java index 1cfddf8..9ba6cca 100755 --- a/src/jalview/appletgui/AlignFrame.java +++ b/src/jalview/appletgui/AlignFrame.java @@ -19,7 +19,6 @@ package jalview.appletgui; -import jalview.jbappletgui.GAlignFrame; import jalview.schemes.*; import jalview.datamodel.*; import jalview.analysis.*; @@ -29,69 +28,88 @@ 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 NEW_WINDOW_WIDTH = 700; + int NEW_WINDOW_HEIGHT = 500; + + String jalviewServletURL; - 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(); + + annotationPanelMenuItem.setState(viewport.showAnnotation); + + seqLimits.setState(viewport.showJVSuffix); if(applet!=null) { - String treeFile = applet.getParameter("treeFile"); - if (treeFile != null) + String param = applet.getParameter("sortBy"); + if (param != null) { - try - { - 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) - { - 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) + param = applet.getParameter("wrap"); + if (param != null) + { + if (param.equalsIgnoreCase("true")) { - ex.printStackTrace(); + wrapMenuItem.setState(true); + wrapMenuItem_actionPerformed(); } } - String param = applet.getParameter("sortBy"); - if (param != null) + try { - if (param.equalsIgnoreCase("Id")) - sortIDMenuItem_actionPerformed(null); - else if (param.equalsIgnoreCase("Pairwise Identity")) - sortPairwiseMenuItem_actionPerformed(null); + param = applet.getParameter("windowWidth"); + if (param != null) + { + int width = Integer.parseInt(param); + NEW_WINDOW_WIDTH = width; + } + param = applet.getParameter("windowHeight"); + if (param != null) + { + int height = Integer.parseInt(param); + NEW_WINDOW_HEIGHT = height; + } } + catch (Exception ex) + {} + } - this.addWindowListener(new WindowAdapter() - { - public void windowClosing(WindowEvent e) - { - closeMenuItem_actionPerformed(null); - } - }); + //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); viewport.addPropertyChangeListener(new java.beans.PropertyChangeListener() { @@ -103,11 +121,404 @@ public class AlignFrame } } }); + + + if(embedded) + { + setEmbedded(); + } + else + { + add(alignPanel, BorderLayout.CENTER); + jalview.bin.JalviewLite.addFrame(this, title, NEW_WINDOW_WIDTH, + NEW_WINDOW_HEIGHT); + } + alignPanel.validate(); + alignPanel.repaint(); + } + 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.repaint(); + } + } - public void inputText_actionPerformed(ActionEvent e) + + public void keyPressed(KeyEvent evt) { - CutAndPasteTransfer cap = new CutAndPasteTransfer(true, applet); + 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() || evt.isMetaDown()) + { + paste(true); + } + 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()); + } + break; + + case KeyEvent.VK_DELETE: + case KeyEvent.VK_BACK_SPACE: + if(viewport.cursorMode) + { + alignPanel.seqPanel.deleteGapAtCursor(evt.isControlDown()); + } + 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; + } + alignPanel.seqPanel.seqCanvas.repaint(); + break; + + case KeyEvent.VK_F: + if (evt.isControlDown()) + { + findMenuItem_actionPerformed(); + } + break; + } + } + 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) + scaleAbove_actionPerformed(); + else if(evt.getSource()==scaleLeft) + scaleLeft_actionPerformed(); + else if(evt.getSource()==scaleRight) + scaleRight_actionPerformed(); + else if(evt.getSource()==seqLimits) + seqLimits_itemStateChanged(); + else if(evt.getSource()==viewBoxesMenuItem) + viewBoxesMenuItem_actionPerformed(); + else if(evt.getSource()==viewTextMenuItem) + viewTextMenuItem_actionPerformed(); + else if(evt.getSource()==renderGapsMenuItem) + renderGapsMenuItem_actionPerformed(); + else if(evt.getSource()==annotationPanelMenuItem) + annotationPanelMenuItem_actionPerformed(); + 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) + applyToAllGroups_actionPerformed(); + else if(evt.getSource()==autoCalculate) + viewport.autocalculateConsensus = autoCalculate.getState(); + } + 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) + remove2LeftMenuItem_actionPerformed(); + else if(source==remove2RightMenuItem) + remove2RightMenuItem_actionPerformed(); + else if(source==removeGappedColumnMenuItem) + removeGappedColumnMenuItem_actionPerformed(); + else if(source==removeAllGapsMenuItem) + removeAllGapsMenuItem_actionPerformed(); + else if(source==findMenuItem) + findMenuItem_actionPerformed(); + else if(source==font) + font_actionPerformed(); + else if(source==showColumns) + { + viewport.showAllHiddenColumns(); alignPanel.repaint(); + } + else if(source==showSeqs) + { + viewport.showAllHiddenSeqs(); alignPanel.repaint(); + } + else if(source == hideColumns) + { + viewport.hideSelectedColumns(); alignPanel.repaint(); + } + else if(source == hideSequences && viewport.getSelectionGroup()!=null) + { + SequenceI[] seqs = viewport.getSelectionGroup().getSequencesInOrder( + viewport.alignment + ); + + for (int i = 0; i < seqs.length; i++) + { + viewport.hideSequence(seqs[i]); + } + + alignPanel.repaint(); + } + else if(source==featureSettings) + featureSettings_actionPerformed(); + else if(source==overviewMenuItem) + overviewMenuItem_actionPerformed(); + else if(source==noColourmenuItem) + noColourmenuItem_actionPerformed(); + else if(source==clustalColour) + clustalColour_actionPerformed(); + else if(source==zappoColour) + zappoColour_actionPerformed(); + else if(source==taylorColour) + taylorColour_actionPerformed(); + else if(source==hydrophobicityColour) + hydrophobicityColour_actionPerformed(); + else if(source==helixColour) + helixColour_actionPerformed(); + else if(source==strandColour) + strandColour_actionPerformed(); + else if(source==turnColour) + turnColour_actionPerformed(); + else if(source==buriedColour) + buriedColour_actionPerformed(); + else if(source==nucleotideColour) + nucleotideColour_actionPerformed(); + else if(source==modifyPID) + modifyPID_actionPerformed(); + else if(source==modifyConservation) + modifyConservation_actionPerformed(); + else if(source==userDefinedColour) + userDefinedColour_actionPerformed(); + else if(source==PIDColour) + PIDColour_actionPerformed(); + else if(source==BLOSUM62Colour) + BLOSUM62Colour_actionPerformed(); + 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); @@ -115,23 +526,87 @@ public class AlignFrame protected void outputText_actionPerformed(ActionEvent e) { - CutAndPasteTransfer cap = new CutAndPasteTransfer(false, applet); + CutAndPasteTransfer cap = new CutAndPasteTransfer(false, 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)); } - public void closeMenuItem_actionPerformed(ActionEvent e) + 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("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() { PaintRefresher.components.remove(viewport.alignment); - dispose(); - if(PaintRefresher.components.size()==0 && applet==null) + if(PaintRefresher.components.size()==0 && viewport.applet==null) System.exit(0); + + this.dispose(); } Stack historyList = new Stack(); @@ -170,7 +645,7 @@ public class AlignFrame updateEditMenuBar(); } - protected void undoMenuItem_actionPerformed(ActionEvent e) + protected void undoMenuItem_actionPerformed() { HistoryItem hi = (HistoryItem) historyList.pop(); redoList.push(new HistoryItem(hi.getDescription(), viewport.alignment, @@ -179,7 +654,7 @@ public class AlignFrame viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences()); } - protected void redoMenuItem_actionPerformed(ActionEvent e) + protected void redoMenuItem_actionPerformed() { HistoryItem hi = (HistoryItem) redoList.pop(); restoreHistoryItem(hi); @@ -190,41 +665,7 @@ public class AlignFrame // used by undo and redo void restoreHistoryItem(HistoryItem hi) { - if (hi.getType() == HistoryItem.SORT) - { - for (int i = 0; i < hi.getSequences().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) - { - // 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); - } - } - } + hi.restore(); updateEditMenuBar(); @@ -244,13 +685,13 @@ 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; } @@ -264,13 +705,13 @@ 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; } @@ -283,8 +724,9 @@ 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) { @@ -294,7 +736,7 @@ 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); @@ -304,7 +746,26 @@ public class AlignFrame int index = 0, startRes, endRes; char ch; - for (int i = 0; i < sg.getSize(); i++) + 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(false); i++) { SequenceI seq = null; @@ -354,12 +815,12 @@ public class AlignFrame } - 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)); @@ -402,7 +863,6 @@ public class AlignFrame 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")) { @@ -412,6 +872,20 @@ public class AlignFrame { newtitle = newtitle.concat("- from " + getTitle()); } + 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, NEW_WINDOW_WIDTH, NEW_WINDOW_HEIGHT); } @@ -428,13 +902,13 @@ 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)); @@ -446,10 +920,10 @@ public class AlignFrame SequenceGroup sg = viewport.getSelectionGroup(); boolean allSequences = false; - if(sg.sequences.size()==viewport.alignment.getHeight()) + if(sg.getSize(false)==viewport.alignment.getHeight()) allSequences = true; - for (int i = 0; i < sg.sequences.size(); i++) + for (int i = 0; i < sg.getSize(false); i++) { SequenceI seq = sg.getSequenceAt(i); int index = viewport.getAlignment().findIndex(seq); @@ -489,7 +963,7 @@ public class AlignFrame } - protected void deleteGroups_actionPerformed(ActionEvent e) + protected void deleteGroups_actionPerformed() { viewport.alignment.deleteAllGroups(); viewport.setSelectionGroup(null); @@ -497,7 +971,7 @@ public class AlignFrame alignPanel.repaint(); } - public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e) + public void selectAllSequenceMenuItem_actionPerformed() { SequenceGroup sg = new SequenceGroup(); for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++) @@ -510,16 +984,23 @@ public class AlignFrame PaintRefresher.Refresh(null, viewport.alignment); } - 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); + alignPanel.idPanel.idCanvas.searchResults = null; + alignPanel.seqPanel.seqCanvas.highlightSearchResults(null); alignPanel.repaint(); PaintRefresher.Refresh(null, viewport.alignment); } - public void invertSequenceMenuItem_actionPerformed(ActionEvent e) + public void invertSequenceMenuItem_actionPerformed() { SequenceGroup sg = viewport.getSelectionGroup(); for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++) @@ -530,7 +1011,7 @@ public class AlignFrame PaintRefresher.Refresh(null, viewport.alignment); } - public void remove2LeftMenuItem_actionPerformed(ActionEvent e) + public void remove2LeftMenuItem_actionPerformed() { ColumnSelection colSel = viewport.getColumnSelection(); if (colSel.size() > 0) @@ -559,7 +1040,7 @@ public class AlignFrame } } - public void remove2RightMenuItem_actionPerformed(ActionEvent e) + public void remove2RightMenuItem_actionPerformed() { ColumnSelection colSel = viewport.getColumnSelection(); if (colSel.size() > 0) @@ -587,7 +1068,7 @@ public class AlignFrame } - public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e) + public void removeGappedColumnMenuItem_actionPerformed() { addHistoryItem(new HistoryItem("Remove Gapped Columns", viewport.alignment, @@ -605,7 +1086,7 @@ public class AlignFrame 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)); @@ -623,10 +1104,10 @@ public class AlignFrame int start=0, end = viewport.alignment.getWidth(); if (viewport.getSelectionGroup() != null - && viewport.getSelectionGroup().sequences != null - && viewport.getSelectionGroup().sequences.size()>0) + && viewport.getSelectionGroup().getSequences(false) != null + && viewport.getSelectionGroup().getSize(false)>0) { - seqs = viewport.getSelectionGroup().sequences; + seqs = viewport.getSelectionGroup().getSequences(true); start = viewport.getSelectionGroup().getStartRes(); end = viewport.getSelectionGroup().getEndRes()+1; } @@ -684,11 +1165,18 @@ public class AlignFrame public void alignmentChanged() { - viewport.updateConsensus(); - viewport.updateConservation (); + viewport.alignment.padGaps(); + if(viewport.autocalculateConsensus) + { + viewport.updateConsensus(); + viewport.updateConservation(); + } + resetAllColourSchemes(); if(alignPanel.overviewPanel!=null) alignPanel.overviewPanel.updateOverviewImage(); + + viewport.alignment.adjustSequenceAnnotations(); alignPanel.repaint(); } @@ -725,7 +1213,8 @@ public class AlignFrame SequenceGroup sg = (SequenceGroup)viewport.alignment.getGroups().elementAt(s); if(sg.cs!=null && sg.cs instanceof ClustalxColourScheme) { - ((ClustalxColourScheme)sg.cs).resetClustalX(sg.sequences, sg.getWidth()); + ((ClustalxColourScheme)sg.cs).resetClustalX( + sg.getSequences(true), sg.getWidth()); } sg.recalcConservation(); } @@ -733,34 +1222,32 @@ public class AlignFrame - 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 font_actionPerformed() { - Frame frame = new Frame(); - FontChooser fc = new FontChooser(alignPanel, frame); - frame.add(fc); - jalview.bin.JalviewLite.addFrame(frame, "Change Font", 440, 100); - + new FontChooser(alignPanel); } - protected void fullSeqId_actionPerformed(ActionEvent e) + + 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()); @@ -770,54 +1257,54 @@ public class AlignFrame alignPanel.repaint(); } - protected void scaleAbove_actionPerformed(ActionEvent e) + protected void scaleAbove_actionPerformed() { viewport.setScaleAboveWrapped(scaleAbove.getState()); alignPanel.repaint(); } - protected void scaleLeft_actionPerformed(ActionEvent e) + protected void scaleLeft_actionPerformed() { viewport.setScaleLeftWrapped(scaleLeft.getState()); alignPanel.repaint(); } - protected void scaleRight_actionPerformed(ActionEvent e) + protected void scaleRight_actionPerformed() { viewport.setScaleRightWrapped(scaleRight.getState()); alignPanel.repaint(); } - public void viewBoxesMenuItem_actionPerformed(ActionEvent e) + public void viewBoxesMenuItem_actionPerformed() { viewport.setShowBoxes(viewBoxesMenuItem.getState()); alignPanel.repaint(); } - public void viewTextMenuItem_actionPerformed(ActionEvent e) + public void viewTextMenuItem_actionPerformed() { viewport.setShowText(viewTextMenuItem.getState()); alignPanel.repaint(); } - protected void renderGapsMenuItem_actionPerformed(ActionEvent e) + protected void renderGapsMenuItem_actionPerformed() { viewport.setRenderGaps(renderGapsMenuItem.getState()); alignPanel.repaint(); } - public void annotationPanelMenuItem_actionPerformed(ActionEvent e) + public void annotationPanelMenuItem_actionPerformed() { - 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 featureSettings_actionPerformed() + { + new FeatureSettings(viewport, alignPanel); + } + + public void overviewMenuItem_actionPerformed() { if (alignPanel.overviewPanel != null) { @@ -845,59 +1332,59 @@ public class AlignFrame } - protected void noColourmenuItem_actionPerformed(ActionEvent e) + protected void noColourmenuItem_actionPerformed() { changeColour(null); } - public void clustalColour_actionPerformed(ActionEvent e) + public void clustalColour_actionPerformed() { abovePIDThreshold.setState(false); changeColour(new ClustalxColourScheme(viewport.alignment.getSequences(), viewport.alignment.getWidth())); } - public void zappoColour_actionPerformed(ActionEvent e) + public void zappoColour_actionPerformed() { changeColour(new ZappoColourScheme()); } - public void taylorColour_actionPerformed(ActionEvent e) + public void taylorColour_actionPerformed() { changeColour(new TaylorColourScheme()); } - public void hydrophobicityColour_actionPerformed(ActionEvent e) + public void hydrophobicityColour_actionPerformed() { changeColour(new HydrophobicColourScheme()); } - public void helixColour_actionPerformed(ActionEvent e) + public void helixColour_actionPerformed() { changeColour(new HelixColourScheme()); } - public void strandColour_actionPerformed(ActionEvent e) + public void strandColour_actionPerformed() { changeColour(new StrandColourScheme()); } - public void turnColour_actionPerformed(ActionEvent e) + public void turnColour_actionPerformed() { changeColour(new TurnColourScheme()); } - public void buriedColour_actionPerformed(ActionEvent e) + public void buriedColour_actionPerformed() { changeColour(new BuriedColourScheme()); } - public void nucleotideColour_actionPerformed(ActionEvent e) + public void nucleotideColour_actionPerformed() { changeColour(new NucleotideColourScheme()); } - protected void applyToAllGroups_actionPerformed(ActionEvent e) + protected void applyToAllGroups_actionPerformed() { viewport.setColourAppliesToAllGroups(applyToAllGroups.getState()); } @@ -963,7 +1450,7 @@ public class AlignFrame } if (cs instanceof ClustalxColourScheme) { - sg.cs = new ClustalxColourScheme(sg.sequences, sg.getWidth()); + sg.cs = new ClustalxColourScheme(sg.getSequences(true), sg.getWidth()); } else { @@ -983,7 +1470,7 @@ 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(true), 0, sg.getWidth())); } else sg.cs.setThreshold(0, viewport.getIgnoreGapsConsensus()); @@ -992,7 +1479,7 @@ public class AlignFrame { 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); @@ -1018,7 +1505,7 @@ public class AlignFrame - protected void modifyPID_actionPerformed(ActionEvent e) + protected void modifyPID_actionPerformed() { if (viewport.getAbovePIDThreshold() && viewport.globalColourScheme!=null) { @@ -1028,7 +1515,7 @@ public class AlignFrame } } - protected void modifyConservation_actionPerformed(ActionEvent e) + protected void modifyConservation_actionPerformed() { if (viewport.getConservationSelected() && viewport.globalColourScheme!=null) { @@ -1038,7 +1525,7 @@ public class AlignFrame } } - protected void conservationMenuItem_actionPerformed(ActionEvent e) + protected void conservationMenuItem_actionPerformed() { viewport.setConservationSelected(conservationMenuItem.getState()); @@ -1047,10 +1534,10 @@ 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()); @@ -1059,25 +1546,25 @@ public class AlignFrame changeColour(viewport.getGlobalColourScheme()); - modifyPID_actionPerformed(null); + modifyPID_actionPerformed(); } - public void userDefinedColour_actionPerformed(ActionEvent e) + public void userDefinedColour_actionPerformed() { - UserDefinedColours chooser = new UserDefinedColours(alignPanel, null); + new UserDefinedColours(alignPanel, null); } - public void PIDColour_actionPerformed(ActionEvent e) + public void PIDColour_actionPerformed() { changeColour(new PIDColourScheme()); } - public void BLOSUM62Colour_actionPerformed(ActionEvent e) + public void BLOSUM62Colour_actionPerformed() { changeColour(new Blosum62ColourScheme()); } - public void sortPairwiseMenuItem_actionPerformed(ActionEvent e) + public void sortPairwiseMenuItem_actionPerformed() { addHistoryItem(new HistoryItem("Pairwise Sort", viewport.alignment, HistoryItem.SORT)); @@ -1086,7 +1573,7 @@ public class AlignFrame alignPanel.repaint(); } - public void sortIDMenuItem_actionPerformed(ActionEvent e) + public void sortIDMenuItem_actionPerformed() { addHistoryItem(new HistoryItem("ID Sort", viewport.alignment, HistoryItem.SORT)); @@ -1094,7 +1581,7 @@ public class AlignFrame alignPanel.repaint(); } - public void sortGroupMenuItem_actionPerformed(ActionEvent e) + public void sortGroupMenuItem_actionPerformed() { addHistoryItem(new HistoryItem("Group Sort", viewport.alignment, HistoryItem.SORT)); @@ -1103,19 +1590,15 @@ public class AlignFrame } - 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(alignPanel)); @@ -1123,12 +1606,30 @@ public class AlignFrame } } - 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; @@ -1136,11 +1637,7 @@ public class AlignFrame try { - PCAPanel pcaPanel = new PCAPanel(viewport); - 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) { @@ -1148,22 +1645,22 @@ 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"); } @@ -1190,23 +1687,39 @@ public class AlignFrame } - 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) @@ -1215,7 +1728,7 @@ 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)); @@ -1233,12 +1746,12 @@ 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 @@ -1269,7 +1782,7 @@ 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); } } @@ -1302,4 +1815,558 @@ public class AlignFrame 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(); + Menu searchMenu = new Menu(); + 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 embeddedSearch; + Label embeddedView; + 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.formats.size(); i++) + { + + item = new MenuItem( (String) jalview.io.AppletFormatAdapter.formats. + elementAt( + 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); + searchMenu.setLabel("Search"); + + 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); + + + alignFrameMenuBar.add(fileMenu); + alignFrameMenuBar.add(editMenu); + alignFrameMenuBar.add(searchMenu); + alignFrameMenuBar.add(viewMenu); + 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(selectAllSequenceMenuItem); + editMenu.add(deselectAllSequenceMenuItem); + editMenu.add(invertSequenceMenuItem); + editMenu.add(invertColSel); + editMenu.add(deleteGroups); + editMenu.addSeparator(); + editMenu.add(remove2LeftMenuItem); + editMenu.add(remove2RightMenuItem); + editMenu.add(removeGappedColumnMenuItem); + editMenu.add(removeAllGapsMenuItem); + editMenu.add(removeRedundancyMenuItem); + searchMenu.add(findMenuItem); + viewMenu.add(font); + viewMenu.addSeparator(); + viewMenu.add(menu1); + viewMenu.add(menu2); + viewMenu.addSeparator(); + viewMenu.add(wrapMenuItem); + viewMenu.add(scaleAbove); + viewMenu.add(scaleLeft); + viewMenu.add(scaleRight); + viewMenu.addSeparator(); + viewMenu.add(seqLimits); + viewMenu.add(viewBoxesMenuItem); + viewMenu.add(viewTextMenuItem); + viewMenu.add(colourTextMenuItem); + viewMenu.add(renderGapsMenuItem); + 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); + } + + public void setEmbedded() + { + + embeddedMenu = new Panel(); + embeddedEdit = new Label(); + embeddedSearch = new Label(); + embeddedView = new Label(); + embeddedColour = new Label(); + embeddedFile = new Label(); + embeddedHelp = new Label(); + embeddedCalculate = new Label(); + flowLayout1 = new FlowLayout(); + embeddedMenu.setBackground(Color.lightGray); + embeddedMenu.setLayout(flowLayout1); + embeddedEdit.setText("Edit"); + embeddedEdit.setFont(new java.awt.Font("Arial", Font.PLAIN, 10)); + embeddedSearch.setText("Search"); + embeddedSearch.setFont(new java.awt.Font("Arial", Font.PLAIN, 10)); + embeddedView.setText("View"); + embeddedView.setFont(new java.awt.Font("Arial", Font.PLAIN, 10)); + embeddedColour.setText("Colour"); + embeddedColour.setFont(new java.awt.Font("Arial", Font.PLAIN, 10)); + embeddedFile.setFont(new java.awt.Font("Arial", Font.PLAIN, 10)); + embeddedFile.setText("File"); + embeddedHelp.setFont(new java.awt.Font("Arial", Font.PLAIN, 10)); + embeddedHelp.setText("Help"); + embeddedCalculate.setFont(new java.awt.Font("Arial", Font.PLAIN, 10)); + embeddedCalculate.setText("Calculate"); + embeddedMenu.add(embeddedFile); + embeddedMenu.add(embeddedEdit); + embeddedMenu.add(embeddedSearch); + embeddedMenu.add(embeddedView); + 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); + embeddedSearch.addMouseListener(this); + embeddedView.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, 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(); + + 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==embeddedSearch) + { + popup = searchPopup = genPopupMenu(searchPopup, searchMenu); + } + else if(source==embeddedView) + { + popup = viewPopup = genPopupMenu(viewPopup, viewMenu); + } + 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