X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FAlignFrame.java;h=c4c2c5bf13fe9d20e6a92efb6e9c2817405d031d;hb=e30c8f0736f711e2dc7c32680ac57a28c77d567d;hp=189a36dbea09b04eb54cd4bf64d06233e308cf34;hpb=1db1f53588cf74844c414838eda44015a5bfdf70;p=jalview.git diff --git a/src/jalview/appletgui/AlignFrame.java b/src/jalview/appletgui/AlignFrame.java index 189a36d..c4c2c5b 100755 --- a/src/jalview/appletgui/AlignFrame.java +++ b/src/jalview/appletgui/AlignFrame.java @@ -172,18 +172,26 @@ public class AlignFrame extends Frame implements ActionListener, StringTokenizer st; SequenceFeature sf; FeatureRenderer fr = alignPanel.seqPanel.seqCanvas.getFeatureRenderer(); - int lineNo = 0; - String featureGroup = null; + 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(); if(type.equalsIgnoreCase("startgroup")) { featureGroup = st.nextToken(); + if (st.hasMoreElements()) + { + groupLink = st.nextToken(); + fr.addFeatureLink(featureGroup, groupLink); + } } else if(type.equalsIgnoreCase("endgroup")) { @@ -191,11 +199,19 @@ public class AlignFrame extends Frame implements ActionListener, //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; } @@ -203,6 +219,7 @@ public class AlignFrame extends Frame implements ActionListener, while (st.hasMoreElements()) { desc = st.nextToken(); + token = st.nextToken(); if (!token.equals("ID_NOT_SPECIFIED")) { @@ -229,9 +246,21 @@ public class AlignFrame extends Frame implements ActionListener, fr.setColour(type, ucs.findColour("A")); } - sf = new SequenceFeature(type, desc, "", start, end, featureGroup); - + 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); } } @@ -248,8 +277,42 @@ public class AlignFrame extends Frame implements ActionListener, } } + 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 @@ -262,6 +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(); @@ -280,21 +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) @@ -335,6 +489,8 @@ public void itemStateChanged(ItemEvent evt) abovePIDThreshold_actionPerformed(); else if(evt.getSource()==applyToAllGroups) applyToAllGroups_actionPerformed(); + else if(evt.getSource()==autoCalculate) + viewport.autocalculateConsensus = autoCalculate.getState(); } public void actionPerformed(ActionEvent evt) { @@ -829,6 +985,11 @@ 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); @@ -1003,8 +1164,13 @@ 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(); @@ -1623,7 +1789,7 @@ public void itemStateChanged(ItemEvent evt) 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); } } @@ -1749,6 +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(); @@ -1926,6 +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); @@ -2021,6 +2190,7 @@ public void itemStateChanged(ItemEvent evt) calculateMenu.addSeparator(); calculateMenu.add(pairwiseAlignmentMenuItem); calculateMenu.add(PCAMenuItem); + calculateMenu.add(autoCalculate); this.add(statusBar, BorderLayout.SOUTH); pasteMenu.add(pasteNew); pasteMenu.add(pasteThis);