X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FAlignFrame.java;h=77154e0b28460ca4d1c0dad0cdf1b4f082cda9bb;hb=cd71fb9ef1a21678ad648ba13564b658b53ab834;hp=dfd58b2c292743a8227a32937bfd3af93752615f;hpb=92c8f4e119ed0b5b362ee9538ef65781dbf50136;p=jalview.git diff --git a/src/jalview/appletgui/AlignFrame.java b/src/jalview/appletgui/AlignFrame.java index dfd58b2..77154e0 100755 --- a/src/jalview/appletgui/AlignFrame.java +++ b/src/jalview/appletgui/AlignFrame.java @@ -41,7 +41,10 @@ public class AlignFrame extends Frame implements ActionListener, jalview.bin.JalviewLite applet; - public AlignFrame(AlignmentI al, jalview.bin.JalviewLite applet, String title) + public AlignFrame(AlignmentI al, + jalview.bin.JalviewLite applet, + String title, + boolean embedded) { try{ jbInit(); @@ -115,9 +118,16 @@ public class AlignFrame extends Frame implements ActionListener, }); - add(alignPanel, BorderLayout.CENTER); - jalview.bin.JalviewLite.addFrame(this, title, NEW_WINDOW_WIDTH, NEW_WINDOW_HEIGHT); - + if(embedded) + { + setEmbedded(); + } + else + { + add(alignPanel, BorderLayout.CENTER); + jalview.bin.JalviewLite.addFrame(this, title, NEW_WINDOW_WIDTH, + NEW_WINDOW_HEIGHT); + } alignPanel.validate(); alignPanel.repaint(); } @@ -140,34 +150,76 @@ public class AlignFrame extends Frame implements ActionListener, public void parseFeaturesFile(String file) { + String line = null; try { - URL url = new URL(file); + BufferedReader in = null; + java.io.InputStream is = getClass().getResourceAsStream("/" + file); + if (is != null) + { + in = new BufferedReader(new java.io.InputStreamReader(is)); + } + else + { + URL url = new URL(file); + in = new BufferedReader(new InputStreamReader(url.openStream())); + } - BufferedReader in = new BufferedReader(new InputStreamReader(url.openStream())); SequenceI seq = null; - String line, type, desc, token; + String type, desc, token; int index, start, end; StringTokenizer st; SequenceFeature sf; FeatureRenderer fr = alignPanel.seqPanel.seqCanvas.getFeatureRenderer(); - int lineNo = 0; + String featureGroup = null, groupLink = null; + Hashtable typeLink = new Hashtable(); + while ( (line = in.readLine()) != null) { - lineNo++; st = new StringTokenizer(line, "\t"); - if (st.countTokens() == 2) + if(!st.hasMoreTokens()) + continue; + + if (st.countTokens() < 4) { type = st.nextToken(); - UserColourScheme ucs = new UserColourScheme(st.nextToken()); - fr.setColour(type, ucs.findColour("A")); + if(type.equalsIgnoreCase("startgroup")) + { + featureGroup = st.nextToken(); + if (st.hasMoreElements()) + { + groupLink = st.nextToken(); + fr.addFeatureLink(featureGroup, groupLink); + } + } + else if(type.equalsIgnoreCase("endgroup")) + { + //We should check whether this is the current group, + //but at present theres no way of showing more than 1 group + st.nextToken(); + featureGroup = null; + groupLink = null; + } + else + { + UserColourScheme ucs = new UserColourScheme(st.nextToken()); + fr.setColour(type, ucs.findColour("A")); + if (st.hasMoreElements()) + { + String link = st.nextToken(); + typeLink.put(type, link); + fr.addFeatureLink(type, link); + } + + } continue; } while (st.hasMoreElements()) { desc = st.nextToken(); + token = st.nextToken(); if (!token.equals("ID_NOT_SPECIFIED")) { @@ -184,8 +236,6 @@ public class AlignFrame extends Frame implements ActionListener, end = Integer.parseInt(st.nextToken()); seq = viewport.alignment.getSequenceAt(index); - start = seq.findIndex(start) - 1; - end = seq.findIndex(end) - 1; type = st.nextToken(); @@ -196,25 +246,73 @@ public class AlignFrame extends Frame implements ActionListener, fr.setColour(type, ucs.findColour("A")); } - sf = new SequenceFeature(type, desc, "", start, end); - + sf = new SequenceFeature(type, desc, start, end, 0f, featureGroup); seq.addSequenceFeature(sf); + + if(groupLink!=null) + { + sf.addLink(groupLink); + sf.description += "%LINK%"; + } + if(typeLink.containsKey(type)) + { + sf.addLink(typeLink.get(type).toString()); + sf.description += "%LINK%"; + } + + parseDescriptionHTML(sf); } } viewport.showSequenceFeatures = true; + sequenceFeatures.setState(true); alignPanel.repaint(); } catch (Exception ex) { - System.out.println("Error parsing groups file: " + ex); + ex.printStackTrace(); + System.out.println("Error parsing groups file: " + ex +"\n"+line); } } + void parseDescriptionHTML(SequenceFeature sf) + { + StringBuffer sb = new StringBuffer(); + StringTokenizer st = new StringTokenizer(sf.getDescription(), "<"); + String token, link; + while(st.hasMoreElements()) + { + token = st.nextToken("<>"); + if(token.equalsIgnoreCase("html") || token.startsWith("/")) + continue; + + if(token.startsWith("a href=")) + { + link = token.substring(token.indexOf("\"")+1, token.length()-1); + String label = st.nextToken("<>"); + sf.addLink(label+"|"+link); + sb.append(label+"%LINK%"); + } + else if(token.equalsIgnoreCase("br")) + sb.append("\n"); + else + sb.append(token); + } + + sf.description = sb.toString(); + } + public void keyPressed(KeyEvent evt) { + if (viewport.cursorMode + && evt.getKeyCode() >= KeyEvent.VK_0 + && evt.getKeyCode() <= KeyEvent.VK_9) + { + alignPanel.seqPanel.numberPressed(evt.getKeyChar()); + } + switch (evt.getKeyCode()) { case 27: // escape key @@ -227,6 +325,10 @@ public class AlignFrame extends Frame implements ActionListener, } break; case KeyEvent.VK_C: + if (viewport.cursorMode) + { + alignPanel.seqPanel.setCursorColumn(); + } if (evt.isControlDown() || evt.isMetaDown()) { copy_actionPerformed(); @@ -245,21 +347,108 @@ public class AlignFrame extends Frame implements ActionListener, } break; case KeyEvent.VK_DOWN: - moveSelectedSequences(false); + if(viewport.cursorMode) + { + alignPanel.seqPanel.moveCursor(0,1); + } + else + moveSelectedSequences(false); break; + case KeyEvent.VK_UP: - moveSelectedSequences(true); + 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; - case KeyEvent.VK_BACK_SPACE: - case KeyEvent.VK_DELETE: - cut_actionPerformed(); - break; } } public void keyReleased(KeyEvent evt) @@ -289,17 +478,26 @@ public void itemStateChanged(ItemEvent evt) 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) { if(evt.getSource()==inputText) inputText_actionPerformed(); + else if(evt.getSource()==loadTree) + loadTree_actionPerformed(); else if(evt.getSource()==closeMenuItem) closeMenuItem_actionPerformed(); else if(evt.getSource()==copy) @@ -346,6 +544,8 @@ public void itemStateChanged(ItemEvent evt) findMenuItem_actionPerformed(); else if(evt.getSource()==font) font_actionPerformed(); + else if(evt.getSource()==featureSettings) + featureSettings_actionPerformed(); else if(evt.getSource()==overviewMenuItem) overviewMenuItem_actionPerformed(); else if(evt.getSource()==noColourmenuItem) @@ -378,6 +578,8 @@ public void itemStateChanged(ItemEvent evt) PIDColour_actionPerformed(); else if(evt.getSource()==BLOSUM62Colour) BLOSUM62Colour_actionPerformed(); + else if(evt.getSource()==annotationColour) + new AnnotationColourChooser(viewport, alignPanel); else if(evt.getSource()==sortPairwiseMenuItem) sortPairwiseMenuItem_actionPerformed(); else if(evt.getSource()==sortIDMenuItem) @@ -407,7 +609,7 @@ public void itemStateChanged(ItemEvent evt) public void inputText_actionPerformed() { - CutAndPasteTransfer cap = new CutAndPasteTransfer(true, applet); + CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this); Frame frame = new Frame(); frame.add(cap); jalview.bin.JalviewLite.addFrame(frame, "Cut & Paste Input", 500, 500); @@ -415,7 +617,7 @@ public void itemStateChanged(ItemEvent evt) 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, @@ -491,41 +693,7 @@ public void itemStateChanged(ItemEvent evt) // 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(); @@ -712,7 +880,10 @@ public void itemStateChanged(ItemEvent evt) { newtitle = newtitle.concat("- from " + getTitle()); } - AlignFrame af = new AlignFrame(new Alignment(newSeqs), applet, newtitle); + AlignFrame af = new AlignFrame(new Alignment(newSeqs), + applet, + newtitle, + false); jalview.bin.JalviewLite.addFrame(af, newtitle, NEW_WINDOW_WIDTH, NEW_WINDOW_HEIGHT); @@ -814,9 +985,15 @@ public void itemStateChanged(ItemEvent evt) 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); @@ -987,11 +1164,18 @@ public void itemStateChanged(ItemEvent evt) 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(); } @@ -1113,6 +1297,11 @@ public void itemStateChanged(ItemEvent evt) alignPanel.setAnnotationVisible(annotationPanelMenuItem.getState()); } + public void featureSettings_actionPerformed() + { + new FeatureSettings(viewport, alignPanel); + } + public void overviewMenuItem_actionPerformed() { if (alignPanel.overviewPanel != null) @@ -1519,7 +1708,28 @@ public void itemStateChanged(ItemEvent evt) jalview.bin.JalviewLite.addFrame(tp, title, 600, 500); } - public void addTreeMenuItem(final TreePanel treePanel, String title) + void loadTree_actionPerformed() + { + TreePanel tp = null; + + 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); + } + + public void loadTree(jalview.io.NewickFile tree, String treeFile) + { + TreePanel tp = new TreePanel(viewport, + viewport.getAlignment().getSequences(), + tree, "From File - ", treeFile); + jalview.bin.JalviewLite.addFrame(tp, treeFile, 600, 500); + addTreeMenuItem(tp, treeFile); + } + + void addTreeMenuItem(final TreePanel treePanel, String title) { final MenuItem item = new MenuItem(title); sortByTreeMenu.add(item); @@ -1638,15 +1848,16 @@ public void itemStateChanged(ItemEvent evt) //JBuilder Graphics here protected MenuBar alignFrameMenuBar = new MenuBar(); - protected Menu fileMenu = new Menu(); - protected MenuItem closeMenuItem = new MenuItem(); - protected Menu editMenu = new Menu(); - protected Menu viewMenu = new Menu(); - protected Menu colourMenu = new Menu(); - protected Menu calculateMenu = new Menu(); - protected MenuItem selectAllSequenceMenuItem = new MenuItem(); - protected MenuItem deselectAllSequenceMenuItem = new MenuItem(); - protected MenuItem invertSequenceMenuItem = new MenuItem(); + protected Menu fileMenu = new Menu("File"); + 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(); @@ -1704,6 +1915,8 @@ public void itemStateChanged(ItemEvent evt) 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(); @@ -1745,19 +1958,11 @@ public void itemStateChanged(ItemEvent evt) outputTextboxMenu.add(item); } - - fileMenu.setLabel("File"); - closeMenuItem.setLabel("Close"); closeMenuItem.addActionListener(this); - editMenu.setLabel("Edit"); - viewMenu.setLabel("View"); - colourMenu.setLabel("Colour"); - calculateMenu.setLabel("Calculate"); - selectAllSequenceMenuItem.setLabel("Select all"); + + loadTree.addActionListener(this); selectAllSequenceMenuItem.addActionListener(this); - deselectAllSequenceMenuItem.setLabel("Deselect All"); deselectAllSequenceMenuItem.addActionListener(this); - invertSequenceMenuItem.setLabel("Invert Selection"); invertSequenceMenuItem.addActionListener(this); remove2LeftMenuItem.setLabel("Remove Left"); remove2LeftMenuItem.addActionListener(this); @@ -1872,6 +2077,7 @@ public void itemStateChanged(ItemEvent evt) font.addActionListener(this); scaleAbove.setLabel("Scale Above"); scaleAbove.setState(true); + scaleAbove.setEnabled(false); scaleAbove.addItemListener(this); scaleLeft.setEnabled(false); scaleLeft.setState(true); @@ -1888,6 +2094,7 @@ public void itemStateChanged(ItemEvent evt) sortByTreeMenu.setLabel("By Tree Order"); sort.setLabel("Sort"); calculate.setLabel("Calculate Tree"); + autoCalculate.addItemListener(this); inputText.setLabel("Input from textbox"); inputText.addActionListener(this); @@ -1900,6 +2107,13 @@ public void itemStateChanged(ItemEvent evt) 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); alignFrameMenuBar.add(fileMenu); alignFrameMenuBar.add(editMenu); @@ -1911,6 +2125,7 @@ public void itemStateChanged(ItemEvent evt) fileMenu.add(inputText); fileMenu.add(outputTextboxMenu); fileMenu.addSeparator(); + fileMenu.add(loadTree); fileMenu.add(closeMenuItem); editMenu.add(undoMenuItem); editMenu.add(redoMenuItem); @@ -1932,7 +2147,7 @@ public void itemStateChanged(ItemEvent evt) searchMenu.add(findMenuItem); viewMenu.add(font); viewMenu.addSeparator(); - viewMenu.add(seqLimits); + viewMenu.add(seqLimits); viewMenu.addSeparator(); viewMenu.add(wrapMenuItem); viewMenu.add(scaleAbove); @@ -1944,7 +2159,10 @@ public void itemStateChanged(ItemEvent evt) viewMenu.add(colourTextMenuItem); viewMenu.add(renderGapsMenuItem); viewMenu.add(annotationPanelMenuItem); - viewMenu.addSeparator(); + viewMenu.addSeparator(); + viewMenu.add(sequenceFeatures); + viewMenu.add(featureSettings); + viewMenu.addSeparator(); viewMenu.add(overviewMenuItem); colourMenu.add(applyToAllGroups); colourMenu.addSeparator(); @@ -1966,11 +2184,13 @@ public void itemStateChanged(ItemEvent evt) colourMenu.add(modifyConservation); colourMenu.add(abovePIDThreshold); colourMenu.add(modifyPID); - calculateMenu.add(sort); + 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); @@ -2032,27 +2252,30 @@ public void itemStateChanged(ItemEvent evt) embeddedCalculate.addMouseListener(this); embeddedHelp.addMouseListener(this); - setVisible(false); + // setVisible(false); fileMenu.remove(closeMenuItem); fileMenu.remove(2); // Seperator applet.setLayout(new BorderLayout()); applet.add(embeddedMenu, BorderLayout.NORTH); applet.add(statusBar, BorderLayout.SOUTH); - applet.validate(); - + // applet.validate(); alignPanel.setSize(applet.size().width, applet.size().height - embeddedMenu.HEIGHT - statusBar.HEIGHT); applet.add(alignPanel, BorderLayout.CENTER); applet.validate(); + } PopupMenu filePopup, editPopup, searchPopup, viewPopup, colourPopup, calculatePopup, helpPopup; + MenuItem featureSettings = new MenuItem(); + CheckboxMenuItem sequenceFeatures = new CheckboxMenuItem(); + MenuItem annotationColour = new MenuItem(); public void mousePressed(MouseEvent evt) {