-/*\r
- * Jalview - A Sequence Alignment Editor and Viewer\r
- * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
- *\r
- * This program is free software; you can redistribute it and/or\r
- * modify it under the terms of the GNU General Public License\r
- * as published by the Free Software Foundation; either version 2\r
- * of the License, or (at your option) any later version.\r
- *\r
- * This program is distributed in the hope that it will be useful,\r
- * but WITHOUT ANY WARRANTY; without even the implied warranty of\r
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\r
- * GNU General Public License for more details.\r
- *\r
- * You should have received a copy of the GNU General Public License\r
- * along with this program; if not, write to the Free Software\r
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
- */\r
-\r
-package jalview.appletgui;\r
-\r
-import jalview.schemes.*;\r
-import jalview.datamodel.*;\r
-import jalview.analysis.*;\r
-import jalview.io.*;\r
-import java.awt.*;\r
-import java.awt.event.*;\r
-import java.util.*;\r
-import java.io.InputStreamReader;\r
-import java.io.BufferedReader;\r
-import java.net.URL;\r
-\r
-\r
-public class AlignFrame extends Frame implements ActionListener,\r
- ItemListener, KeyListener, MouseListener\r
-{\r
- public AlignmentPanel alignPanel;\r
- public AlignViewport viewport;\r
- int NEW_WINDOW_WIDTH = 700;\r
- int NEW_WINDOW_HEIGHT = 500;\r
-\r
- String jalviewServletURL;\r
-\r
-\r
- public AlignFrame(AlignmentI al,\r
- jalview.bin.JalviewLite applet,\r
- String title,\r
- boolean embedded)\r
- {\r
-\r
- jalviewServletURL = applet.getParameter("APPLICATION_URL");\r
-\r
- try{\r
- jbInit();\r
- }catch(Exception ex)\r
- {\r
- ex.printStackTrace();\r
- }\r
-\r
- viewport = new AlignViewport(al, applet);\r
- alignPanel = new AlignmentPanel(this, viewport);\r
-\r
- annotationPanelMenuItem.setState(viewport.showAnnotation);\r
-\r
- seqLimits.setState(viewport.showJVSuffix);\r
-\r
- if(applet!=null)\r
- {\r
- String param = applet.getParameter("sortBy");\r
- if (param != null)\r
- {\r
- if (param.equalsIgnoreCase("Id"))\r
- sortIDMenuItem_actionPerformed();\r
- else if (param.equalsIgnoreCase("Pairwise Identity"))\r
- sortPairwiseMenuItem_actionPerformed();\r
- }\r
-\r
- param = applet.getParameter("wrap");\r
- if (param != null)\r
- {\r
- if (param.equalsIgnoreCase("true"))\r
- {\r
- wrapMenuItem.setState(true);\r
- wrapMenuItem_actionPerformed();\r
- }\r
- }\r
-\r
- try\r
- {\r
- param = applet.getParameter("windowWidth");\r
- if (param != null)\r
- {\r
- int width = Integer.parseInt(param);\r
- NEW_WINDOW_WIDTH = width;\r
- }\r
- param = applet.getParameter("windowHeight");\r
- if (param != null)\r
- {\r
- int height = Integer.parseInt(param);\r
- NEW_WINDOW_HEIGHT = height;\r
- }\r
- }\r
- catch (Exception ex)\r
- {}\r
-\r
- }\r
-\r
- //Some JVMS send keyevents to Top frame or lowest panel,\r
- //Havent worked out why yet. So add to both this frame and seqCanvas for now\r
- this.addKeyListener(this);\r
- alignPanel.seqPanel.seqCanvas.addKeyListener(this);\r
- alignPanel.idPanel.idCanvas.addKeyListener(this);\r
-\r
- viewport.addPropertyChangeListener(new java.beans.PropertyChangeListener()\r
- {\r
- public void propertyChange(java.beans.PropertyChangeEvent evt)\r
- {\r
- if (evt.getPropertyName().equals("alignment"))\r
- {\r
- alignmentChanged();\r
- }\r
- }\r
- });\r
-\r
-\r
- if(embedded)\r
- {\r
- setEmbedded();\r
- }\r
- else\r
- {\r
- add(alignPanel, BorderLayout.CENTER);\r
- jalview.bin.JalviewLite.addFrame(this, title, NEW_WINDOW_WIDTH,\r
- NEW_WINDOW_HEIGHT);\r
- }\r
- alignPanel.validate();\r
- alignPanel.repaint();\r
- }\r
- public AlignViewport getAlignViewport()\r
- {\r
- return viewport;\r
- }\r
-\r
- public SeqCanvas getSeqcanvas()\r
- {\r
- return alignPanel.seqPanel.seqCanvas;\r
- }\r
-\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param String DOCUMENT ME!\r
- */\r
-\r
- public void parseFeaturesFile(String file, String type)\r
- {\r
- Hashtable featureLinks = new Hashtable();\r
- boolean featuresFile = false;\r
- try{\r
- featuresFile = new jalview.io.FeaturesFile(file, type).parse(viewport.alignment,\r
- alignPanel.seqPanel.seqCanvas.\r
- getFeatureRenderer().featureColours,\r
- featureLinks,\r
- true);\r
- }\r
- catch(Exception ex)\r
- {\r
- ex.printStackTrace();\r
- }\r
-\r
- if(featuresFile)\r
- {\r
- if(featureLinks.size()>0)\r
- alignPanel.seqPanel.seqCanvas\r
- .getFeatureRenderer().featureLinks = featureLinks;\r
- viewport.showSequenceFeatures = true;\r
- sequenceFeatures.setState(true);\r
- alignPanel.repaint();\r
- }\r
-\r
- }\r
-\r
-\r
- public void keyPressed(KeyEvent evt)\r
- {\r
- if (viewport.cursorMode\r
- && evt.getKeyCode() >= KeyEvent.VK_0\r
- && evt.getKeyCode() <= KeyEvent.VK_9)\r
- {\r
- alignPanel.seqPanel.numberPressed(evt.getKeyChar());\r
- }\r
-\r
- switch (evt.getKeyCode())\r
- {\r
- case 27: // escape key\r
- deselectAllSequenceMenuItem_actionPerformed();\r
- break;\r
- case KeyEvent.VK_X:\r
- if (evt.isControlDown() || evt.isMetaDown())\r
- {\r
- cut_actionPerformed();\r
- }\r
- break;\r
- case KeyEvent.VK_C:\r
- if (viewport.cursorMode && !evt.isControlDown())\r
- {\r
- alignPanel.seqPanel.setCursorColumn();\r
- }\r
- if (evt.isControlDown() || evt.isMetaDown())\r
- {\r
- copy_actionPerformed();\r
- }\r
- break;\r
- case KeyEvent.VK_V:\r
- if (evt.isControlDown() || evt.isMetaDown())\r
- {\r
- paste(true);\r
- }\r
- break;\r
- case KeyEvent.VK_A:\r
- if (evt.isControlDown() || evt.isMetaDown())\r
- {\r
- selectAllSequenceMenuItem_actionPerformed();\r
- }\r
- break;\r
- case KeyEvent.VK_DOWN:\r
- if(viewport.cursorMode)\r
- {\r
- alignPanel.seqPanel.moveCursor(0,1);\r
- }\r
- else\r
- moveSelectedSequences(false);\r
- break;\r
-\r
- case KeyEvent.VK_UP:\r
- if (viewport.cursorMode)\r
- {\r
- alignPanel.seqPanel.moveCursor(0,-1);\r
- }\r
- else\r
- moveSelectedSequences(true);\r
- break;\r
-\r
- case KeyEvent.VK_LEFT:\r
- if(viewport.cursorMode)\r
- {\r
- alignPanel.seqPanel.moveCursor(-1,0);\r
- }\r
- break;\r
-\r
- case KeyEvent.VK_RIGHT:\r
- if (viewport.cursorMode)\r
- {\r
- alignPanel.seqPanel.moveCursor(1,0);\r
- }\r
- break;\r
- case KeyEvent.VK_SPACE:\r
- if(viewport.cursorMode)\r
- {\r
- alignPanel.seqPanel.insertGapAtCursor(evt.isControlDown());\r
- }\r
- break;\r
-\r
- case KeyEvent.VK_DELETE:\r
- case KeyEvent.VK_BACK_SPACE:\r
- if(viewport.cursorMode)\r
- {\r
- alignPanel.seqPanel.deleteGapAtCursor(evt.isControlDown());\r
- }\r
- else\r
- {\r
- cut_actionPerformed();\r
- alignPanel.seqPanel.seqCanvas.repaint();\r
- }\r
- break;\r
-\r
- case KeyEvent.VK_S:\r
- if(viewport.cursorMode)\r
- {\r
- alignPanel.seqPanel.setCursorRow();\r
- }\r
- break;\r
- case KeyEvent.VK_P:\r
- if(viewport.cursorMode)\r
- {\r
- alignPanel.seqPanel.setCursorPosition();\r
- }\r
- break;\r
-\r
- case KeyEvent.VK_ENTER:\r
- case KeyEvent.VK_COMMA:\r
- if(viewport.cursorMode)\r
- {\r
- alignPanel.seqPanel.setCursorRowAndColumn();\r
- }\r
- break;\r
-\r
- case KeyEvent.VK_Q:\r
- if(viewport.cursorMode)\r
- {\r
- alignPanel.seqPanel.setSelectionAreaAtCursor(true);\r
- }\r
- break;\r
- case KeyEvent.VK_M:\r
- if(viewport.cursorMode)\r
- {\r
- alignPanel.seqPanel.setSelectionAreaAtCursor(false);\r
- }\r
- break;\r
-\r
- case KeyEvent.VK_F2:\r
- viewport.cursorMode = ! viewport.cursorMode;\r
- statusBar.setText("Keyboard editing mode is "+\r
- (viewport.cursorMode ? "on" : "off"));\r
- if(viewport.cursorMode)\r
- {\r
- alignPanel.seqPanel.seqCanvas.cursorX = viewport.startRes;\r
- alignPanel.seqPanel.seqCanvas.cursorY = viewport.startSeq;\r
- }\r
- alignPanel.seqPanel.seqCanvas.repaint();\r
- break;\r
-\r
- case KeyEvent.VK_F:\r
- if (evt.isControlDown())\r
- {\r
- findMenuItem_actionPerformed();\r
- }\r
- break;\r
- }\r
- }\r
- public void keyReleased(KeyEvent evt)\r
- {}\r
- public void keyTyped(KeyEvent evt)\r
- {}\r
-\r
-public void itemStateChanged(ItemEvent evt)\r
- {\r
- if(evt.getSource()==colourTextMenuItem)\r
- colourTextMenuItem_actionPerformed();\r
- else if(evt.getSource()==wrapMenuItem)\r
- wrapMenuItem_actionPerformed();\r
- else if(evt.getSource()==scaleAbove)\r
- scaleAbove_actionPerformed();\r
- else if(evt.getSource()==scaleLeft)\r
- scaleLeft_actionPerformed();\r
- else if(evt.getSource()==scaleRight)\r
- scaleRight_actionPerformed();\r
- else if(evt.getSource()==seqLimits)\r
- seqLimits_itemStateChanged();\r
- else if(evt.getSource()==viewBoxesMenuItem)\r
- viewBoxesMenuItem_actionPerformed();\r
- else if(evt.getSource()==viewTextMenuItem)\r
- viewTextMenuItem_actionPerformed();\r
- else if(evt.getSource()==renderGapsMenuItem)\r
- renderGapsMenuItem_actionPerformed();\r
- else if(evt.getSource()==annotationPanelMenuItem)\r
- annotationPanelMenuItem_actionPerformed();\r
- else if(evt.getSource()==sequenceFeatures)\r
- {\r
- viewport.showSequenceFeatures(sequenceFeatures.getState());\r
- alignPanel.seqPanel.seqCanvas.repaint();\r
- }\r
- else if(evt.getSource()==conservationMenuItem)\r
- conservationMenuItem_actionPerformed();\r
- else if(evt.getSource()==abovePIDThreshold)\r
- abovePIDThreshold_actionPerformed();\r
- else if(evt.getSource()==applyToAllGroups)\r
- applyToAllGroups_actionPerformed();\r
- else if(evt.getSource()==autoCalculate)\r
- viewport.autocalculateConsensus = autoCalculate.getState();\r
- }\r
- public void actionPerformed(ActionEvent evt)\r
- {\r
- if(evt.getSource()==inputText)\r
- inputText_actionPerformed();\r
- else if(evt.getSource()==loadTree)\r
- loadTree_actionPerformed();\r
- else if(evt.getSource()==loadApplication)\r
- launchFullApplication();\r
- else if(evt.getSource()==closeMenuItem)\r
- closeMenuItem_actionPerformed();\r
- else if(evt.getSource()==copy)\r
- copy_actionPerformed();\r
- else if(evt.getSource()==undoMenuItem)\r
- undoMenuItem_actionPerformed();\r
- else if(evt.getSource()==redoMenuItem)\r
- redoMenuItem_actionPerformed();\r
- else if(evt.getSource()==inputText)\r
- inputText_actionPerformed();\r
- else if(evt.getSource()==closeMenuItem)\r
- closeMenuItem_actionPerformed();\r
- else if(evt.getSource()==undoMenuItem)\r
- undoMenuItem_actionPerformed();\r
- else if(evt.getSource()==redoMenuItem)\r
- redoMenuItem_actionPerformed();\r
- else if(evt.getSource()==copy)\r
- copy_actionPerformed();\r
- else if(evt.getSource()==pasteNew)\r
- pasteNew_actionPerformed();\r
- else if(evt.getSource()==pasteThis)\r
- pasteThis_actionPerformed();\r
- else if(evt.getSource()==cut)\r
- cut_actionPerformed();\r
- else if(evt.getSource()==delete)\r
- delete_actionPerformed();\r
- else if(evt.getSource()==deleteGroups)\r
- deleteGroups_actionPerformed();\r
- else if(evt.getSource()==selectAllSequenceMenuItem)\r
- selectAllSequenceMenuItem_actionPerformed();\r
- else if(evt.getSource()==deselectAllSequenceMenuItem)\r
- deselectAllSequenceMenuItem_actionPerformed();\r
- else if(evt.getSource()==invertSequenceMenuItem)\r
- invertSequenceMenuItem_actionPerformed();\r
- else if(evt.getSource()==remove2LeftMenuItem)\r
- remove2LeftMenuItem_actionPerformed();\r
- else if(evt.getSource()==remove2RightMenuItem)\r
- remove2RightMenuItem_actionPerformed();\r
- else if(evt.getSource()==removeGappedColumnMenuItem)\r
- removeGappedColumnMenuItem_actionPerformed();\r
- else if(evt.getSource()==removeAllGapsMenuItem)\r
- removeAllGapsMenuItem_actionPerformed();\r
- else if(evt.getSource()==findMenuItem)\r
- findMenuItem_actionPerformed();\r
- else if(evt.getSource()==font)\r
- font_actionPerformed();\r
- else if(evt.getSource()==featureSettings)\r
- featureSettings_actionPerformed();\r
- else if(evt.getSource()==overviewMenuItem)\r
- overviewMenuItem_actionPerformed();\r
- else if(evt.getSource()==noColourmenuItem)\r
- noColourmenuItem_actionPerformed();\r
- else if(evt.getSource()==clustalColour)\r
- clustalColour_actionPerformed();\r
- else if(evt.getSource()==zappoColour)\r
- zappoColour_actionPerformed();\r
- else if(evt.getSource()==taylorColour)\r
- taylorColour_actionPerformed();\r
- else if(evt.getSource()==hydrophobicityColour)\r
- hydrophobicityColour_actionPerformed();\r
- else if(evt.getSource()==helixColour)\r
- helixColour_actionPerformed();\r
- else if(evt.getSource()==strandColour)\r
- strandColour_actionPerformed();\r
- else if(evt.getSource()==turnColour)\r
- turnColour_actionPerformed();\r
- else if(evt.getSource()==buriedColour)\r
- buriedColour_actionPerformed();\r
- else if(evt.getSource()==nucleotideColour)\r
- nucleotideColour_actionPerformed();\r
- else if(evt.getSource()==modifyPID)\r
- modifyPID_actionPerformed();\r
- else if(evt.getSource()==modifyConservation)\r
- modifyConservation_actionPerformed();\r
- else if(evt.getSource()==userDefinedColour)\r
- userDefinedColour_actionPerformed();\r
- else if(evt.getSource()==PIDColour)\r
- PIDColour_actionPerformed();\r
- else if(evt.getSource()==BLOSUM62Colour)\r
- BLOSUM62Colour_actionPerformed();\r
- else if(evt.getSource()==annotationColour)\r
- new AnnotationColourChooser(viewport, alignPanel);\r
- else if(evt.getSource()==sortPairwiseMenuItem)\r
- sortPairwiseMenuItem_actionPerformed();\r
- else if(evt.getSource()==sortIDMenuItem)\r
- sortIDMenuItem_actionPerformed();\r
- else if(evt.getSource()==sortGroupMenuItem)\r
- sortGroupMenuItem_actionPerformed();\r
- else if(evt.getSource()==removeRedundancyMenuItem)\r
- removeRedundancyMenuItem_actionPerformed();\r
- else if(evt.getSource()==pairwiseAlignmentMenuItem)\r
- pairwiseAlignmentMenuItem_actionPerformed();\r
- else if(evt.getSource()==PCAMenuItem)\r
- PCAMenuItem_actionPerformed();\r
- else if(evt.getSource()==averageDistanceTreeMenuItem)\r
- averageDistanceTreeMenuItem_actionPerformed();\r
- else if(evt.getSource()==neighbourTreeMenuItem)\r
- neighbourTreeMenuItem_actionPerformed();\r
- else if(evt.getSource()==njTreeBlosumMenuItem)\r
- njTreeBlosumMenuItem_actionPerformed();\r
- else if(evt.getSource()==avDistanceTreeBlosumMenuItem)\r
- avTreeBlosumMenuItem_actionPerformed();\r
- else if(evt.getSource()==documentation)\r
- documentation_actionPerformed();\r
- else if(evt.getSource()==about)\r
- about_actionPerformed();\r
-\r
- }\r
-\r
- public void inputText_actionPerformed()\r
- {\r
- CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);\r
- Frame frame = new Frame();\r
- frame.add(cap);\r
- jalview.bin.JalviewLite.addFrame(frame, "Cut & Paste Input", 500, 500);\r
- }\r
-\r
- protected void outputText_actionPerformed(ActionEvent e)\r
- {\r
- CutAndPasteTransfer cap = new CutAndPasteTransfer(false, this);\r
- Frame frame = new Frame();\r
- frame.add(cap);\r
- jalview.bin.JalviewLite.addFrame(frame,\r
- "Alignment output - " + e.getActionCommand(),\r
- 600, 500);\r
- cap.setText(new AppletFormatAdapter().formatSequences(e.getActionCommand(),\r
- viewport.getAlignment().getSequences(),\r
- viewport.showJVSuffix));\r
- }\r
-\r
- void launchFullApplication()\r
- {\r
- StringBuffer url = new StringBuffer(jalviewServletURL);\r
-\r
- url.append("?open="+\r
- appendProtocol( viewport.applet.getParameter("file") ) );\r
-\r
- if(viewport.applet.getParameter("features")!=null)\r
- {\r
- url.append( "&features=" );\r
- url.append( appendProtocol( viewport.applet.getParameter("features") ) );\r
- }\r
-\r
- if(viewport.applet.getParameter("annotations")!=null)\r
- {\r
- url.append( "&annotations=" );\r
- url.append( appendProtocol( viewport.applet.getParameter("annotations") ) );\r
- }\r
-\r
- if(viewport.applet.getParameter("defaultColour")!=null)\r
- {\r
- url.append("&colour=" +\r
- removeWhiteSpace(viewport.applet.getParameter("defaultColour"))\r
- );\r
- }\r
-\r
- if(viewport.applet.getParameter("userDefinedColour")!=null)\r
- {\r
- url.append( "&colour=" +\r
- removeWhiteSpace( viewport.applet.getParameter("userDefinedColour") )\r
- );\r
- }\r
-\r
- showURL(url.toString(), "FULL_APP");\r
- }\r
-\r
-\r
- String removeWhiteSpace(String colour)\r
- {\r
- StringBuffer sb = new StringBuffer();\r
- for (int i = 0; i < colour.length(); i++)\r
- {\r
- if (Character.isWhitespace(colour.charAt(i)))\r
- sb.append("%20");\r
- else\r
- sb.append(colour.charAt(i));\r
- }\r
-\r
- return sb.toString();\r
- }\r
-\r
-\r
- String appendProtocol(String url)\r
- {\r
- try{\r
- new URL(url);\r
- }catch(java.net.MalformedURLException ex)\r
- {\r
- url = viewport.applet.getCodeBase()+url;\r
- }\r
- return url;\r
- }\r
-\r
- public void closeMenuItem_actionPerformed()\r
- {\r
- PaintRefresher.components.remove(viewport.alignment);\r
- if(PaintRefresher.components.size()==0 && viewport.applet==null)\r
- System.exit(0);\r
-\r
- this.dispose();\r
- }\r
-\r
- Stack historyList = new Stack();\r
- Stack redoList = new Stack();\r
-\r
- void updateEditMenuBar()\r
- {\r
- if (historyList.size() > 0)\r
- {\r
- undoMenuItem.setEnabled(true);\r
- HistoryItem hi = (HistoryItem) historyList.peek();\r
- undoMenuItem.setLabel("Undo " + hi.getDescription());\r
- }\r
- else\r
- {\r
- undoMenuItem.setEnabled(false);\r
- undoMenuItem.setLabel("Undo");\r
- }\r
-\r
- if (redoList.size() > 0)\r
- {\r
- redoMenuItem.setEnabled(true);\r
- HistoryItem hi = (HistoryItem) redoList.peek();\r
- redoMenuItem.setLabel("Redo " + hi.getDescription());\r
- }\r
- else\r
- {\r
- redoMenuItem.setEnabled(false);\r
- redoMenuItem.setLabel("Redo");\r
- }\r
- }\r
-\r
- public void addHistoryItem(HistoryItem hi)\r
- {\r
- historyList.push(hi);\r
- updateEditMenuBar();\r
- }\r
-\r
- protected void undoMenuItem_actionPerformed()\r
- {\r
- HistoryItem hi = (HistoryItem) historyList.pop();\r
- redoList.push(new HistoryItem(hi.getDescription(), viewport.alignment,\r
- HistoryItem.HIDE));\r
- restoreHistoryItem(hi);\r
- viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());\r
- }\r
-\r
- protected void redoMenuItem_actionPerformed()\r
- {\r
- HistoryItem hi = (HistoryItem) redoList.pop();\r
- restoreHistoryItem(hi);\r
- updateEditMenuBar();\r
- viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());\r
- }\r
-\r
- // used by undo and redo\r
- void restoreHistoryItem(HistoryItem hi)\r
- {\r
- hi.restore();\r
-\r
- updateEditMenuBar();\r
-\r
- viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());\r
- }\r
-\r
- public void moveSelectedSequences(boolean up)\r
- {\r
- SequenceGroup sg = viewport.getSelectionGroup();\r
- if (sg == null)\r
- {\r
- return;\r
- }\r
-\r
- if (up)\r
- {\r
- for (int i = 1; i < viewport.alignment.getHeight(); i++)\r
- {\r
- SequenceI seq = viewport.alignment.getSequenceAt(i);\r
- if (!sg.getSequences(false).contains(seq))\r
- {\r
- continue;\r
- }\r
-\r
- SequenceI temp = viewport.alignment.getSequenceAt(i - 1);\r
- if (sg.getSequences(false).contains(temp))\r
- {\r
- continue;\r
- }\r
-\r
- viewport.alignment.getSequences().setElementAt(temp, i);\r
- viewport.alignment.getSequences().setElementAt(seq, i - 1);\r
- }\r
- }\r
- else\r
- {\r
- for (int i = viewport.alignment.getHeight() - 2; i > -1; i--)\r
- {\r
- SequenceI seq = viewport.alignment.getSequenceAt(i);\r
- if (!sg.getSequences(true).contains(seq))\r
- {\r
- continue;\r
- }\r
-\r
- SequenceI temp = viewport.alignment.getSequenceAt(i + 1);\r
- if (sg.getSequences(true).contains(temp))\r
- {\r
- continue;\r
- }\r
-\r
- viewport.alignment.getSequences().setElementAt(temp, i);\r
- viewport.alignment.getSequences().setElementAt(seq, i + 1);\r
- }\r
- }\r
-\r
- alignPanel.repaint();\r
- }\r
-\r
- static StringBuffer copiedSequences;\r
- static Vector copiedHiddenColumns;\r
- protected void copy_actionPerformed()\r
- {\r
- if (viewport.getSelectionGroup() == null)\r
- {\r
- return;\r
- }\r
-\r
- SequenceGroup sg = viewport.getSelectionGroup();\r
- copiedSequences = new StringBuffer();\r
- Hashtable orderedSeqs = new Hashtable();\r
- for (int i = 0; i < sg.getSize(false); i++)\r
- {\r
- SequenceI seq = sg.getSequenceAt(i);\r
- int index = viewport.alignment.findIndex(seq);\r
- orderedSeqs.put(index + "", seq);\r
- }\r
-\r
- int index = 0, startRes, endRes;\r
- char ch;\r
-\r
- if (viewport.hasHiddenColumns && viewport.getSelectionGroup() != null)\r
- {\r
- copiedHiddenColumns = new Vector();\r
- int hiddenOffset = viewport.getSelectionGroup().getStartRes();\r
- for (int i = 0; i < viewport.getColumnSelection().getHiddenColumns().size();\r
- i++)\r
- {\r
- int[] region = (int[])\r
- viewport.getColumnSelection().getHiddenColumns().elementAt(i);\r
-\r
- copiedHiddenColumns.addElement(new int[]\r
- {region[0] - hiddenOffset,\r
- region[1] - hiddenOffset});\r
- }\r
- }\r
- else\r
- copiedHiddenColumns = null;\r
-\r
-\r
- for (int i = 0; i < sg.getSize(false); i++)\r
- {\r
- SequenceI seq = null;\r
-\r
- while (seq == null)\r
- {\r
- if (orderedSeqs.containsKey(index + ""))\r
- {\r
- seq = (SequenceI) orderedSeqs.get(index + "");\r
- index++;\r
-\r
- break;\r
- }\r
- else\r
- {\r
- index++;\r
- }\r
- }\r
-\r
- //FIND START RES\r
- //Returns residue following index if gap\r
- startRes = seq.findPosition(sg.getStartRes());\r
-\r
- //FIND END RES\r
- //Need to find the residue preceeding index if gap\r
- endRes = 0;\r
-\r
- for (int j = 0; j < sg.getEndRes()+1 && j < seq.getLength(); j++)\r
- {\r
- ch = seq.getCharAt(j);\r
- if (!jalview.util.Comparison.isGap( (ch)))\r
- {\r
- endRes++;\r
- }\r
- }\r
-\r
- if(endRes>0)\r
- {\r
- endRes += seq.getStart() -1;\r
- }\r
-\r
- copiedSequences.append(seq.getName() + "\t" +\r
- startRes + "\t" +\r
- endRes + "\t" +\r
- seq.getSequence(sg.getStartRes(),\r
- sg.getEndRes() + 1) + "\n");\r
- }\r
-\r
- }\r
-\r
- protected void pasteNew_actionPerformed()\r
- {\r
- paste(true);\r
- }\r
-\r
- protected void pasteThis_actionPerformed()\r
- {\r
- addHistoryItem(new HistoryItem("Paste Sequences", viewport.alignment,\r
- HistoryItem.PASTE));\r
- paste(false);\r
- }\r
-\r
- void paste(boolean newAlignment)\r
- {\r
- try\r
- {\r
- if (copiedSequences == null)\r
- {\r
- return;\r
- }\r
-\r
- StringTokenizer st = new StringTokenizer(copiedSequences.toString());\r
- Vector seqs = new Vector();\r
- while (st.hasMoreElements())\r
- {\r
- String name = st.nextToken();\r
- int start = Integer.parseInt(st.nextToken());\r
- int end = Integer.parseInt(st.nextToken());\r
- Sequence sequence = new Sequence(name, st.nextToken(), start, end);\r
-\r
- if (!newAlignment)\r
- {\r
- viewport.alignment.addSequence(sequence);\r
- }\r
- else\r
- {\r
- seqs.addElement(sequence);\r
- }\r
- }\r
-\r
- if (newAlignment)\r
- {\r
- SequenceI[] newSeqs = new SequenceI[seqs.size()];\r
- for (int i = 0; i < seqs.size(); i++)\r
- {\r
- newSeqs[i] = (SequenceI) seqs.elementAt(i);\r
- }\r
-\r
- String newtitle = new String("Copied sequences");\r
- if (getTitle().startsWith("Copied sequences"))\r
- {\r
- newtitle = getTitle();\r
- }\r
- else\r
- {\r
- newtitle = newtitle.concat("- from " + getTitle());\r
- }\r
- AlignFrame af = new AlignFrame(new Alignment(newSeqs),\r
- viewport.applet,\r
- newtitle,\r
- false);\r
- if (copiedHiddenColumns != null)\r
- {\r
- for (int i = 0; i < copiedHiddenColumns.size(); i++)\r
- {\r
- int[] region = (int[]) copiedHiddenColumns.elementAt(i);\r
- af.viewport.hideColumns(region[0], region[1]);\r
- }\r
- }\r
-\r
-\r
- jalview.bin.JalviewLite.addFrame(af, newtitle, NEW_WINDOW_WIDTH,\r
- NEW_WINDOW_HEIGHT);\r
- }\r
- else\r
- {\r
- viewport.setEndSeq(viewport.alignment.getHeight());\r
- viewport.alignment.getWidth();\r
- viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());\r
- }\r
-\r
- }\r
- catch (Exception ex)\r
- {} // could be anything being pasted in here\r
-\r
- }\r
-\r
- protected void cut_actionPerformed()\r
- {\r
- copy_actionPerformed();\r
- delete_actionPerformed();\r
- }\r
-\r
- protected void delete_actionPerformed()\r
- {\r
- addHistoryItem(new HistoryItem("Delete Sequences", viewport.alignment,\r
- HistoryItem.HIDE));\r
- if (viewport.getSelectionGroup() == null)\r
- {\r
- return;\r
- }\r
-\r
-\r
- SequenceGroup sg = viewport.getSelectionGroup();\r
- boolean allSequences = false;\r
- if(sg.getSize(false)==viewport.alignment.getHeight())\r
- allSequences = true;\r
-\r
- for (int i = 0; i < sg.getSize(false); i++)\r
- {\r
- SequenceI seq = sg.getSequenceAt(i);\r
- int index = viewport.getAlignment().findIndex(seq);\r
- seq.deleteChars(sg.getStartRes(), sg.getEndRes() + 1);\r
-\r
- // If the cut affects all sequences, remove highlighted columns\r
- if (allSequences)\r
- {\r
- viewport.getColumnSelection().removeElements(sg.getStartRes(),\r
- sg.getEndRes() + 1);\r
- }\r
-\r
-\r
- if (seq.getSequence().length() < 1)\r
- {\r
- viewport.getAlignment().deleteSequence(seq);\r
- }\r
- else\r
- {\r
- viewport.getAlignment().getSequences().setElementAt(seq, index);\r
- }\r
- }\r
-\r
- viewport.setSelectionGroup(null);\r
- viewport.alignment.deleteGroup(sg);\r
- viewport.resetSeqLimits(alignPanel.seqPanel.seqCanvas.getSize().height);\r
- if (viewport.getAlignment().getHeight() < 1)\r
- {\r
- try\r
- {\r
- this.setVisible(false);\r
- }\r
- catch (Exception ex)\r
- {}\r
- }\r
- viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());\r
-\r
- }\r
-\r
- protected void deleteGroups_actionPerformed()\r
- {\r
- viewport.alignment.deleteAllGroups();\r
- viewport.setSelectionGroup(null);\r
-\r
- alignPanel.repaint();\r
- }\r
-\r
- public void selectAllSequenceMenuItem_actionPerformed()\r
- {\r
- SequenceGroup sg = new SequenceGroup();\r
- for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)\r
- {\r
- sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);\r
- }\r
- sg.setEndRes(viewport.alignment.getWidth()-1);\r
- viewport.setSelectionGroup(sg);\r
- alignPanel.repaint();\r
- PaintRefresher.Refresh(null, viewport.alignment);\r
- }\r
-\r
- public void deselectAllSequenceMenuItem_actionPerformed()\r
- {\r
- if(viewport.cursorMode)\r
- {\r
- alignPanel.seqPanel.keyboardNo1=null;\r
- alignPanel.seqPanel.keyboardNo2=null;\r
- }\r
- viewport.setSelectionGroup(null);\r
- viewport.getColumnSelection().clear();\r
- viewport.setSelectionGroup(null);\r
- alignPanel.idPanel.idCanvas.searchResults = null;\r
- alignPanel.seqPanel.seqCanvas.highlightSearchResults(null);\r
- alignPanel.repaint();\r
- PaintRefresher.Refresh(null, viewport.alignment);\r
- }\r
-\r
- public void invertSequenceMenuItem_actionPerformed()\r
- {\r
- SequenceGroup sg = viewport.getSelectionGroup();\r
- for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)\r
- {\r
- sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);\r
- }\r
-\r
- PaintRefresher.Refresh(null, viewport.alignment);\r
- }\r
-\r
- public void remove2LeftMenuItem_actionPerformed()\r
- {\r
- ColumnSelection colSel = viewport.getColumnSelection();\r
- if (colSel.size() > 0)\r
- {\r
- addHistoryItem(new HistoryItem("Remove Left", viewport.alignment,\r
- HistoryItem.HIDE));\r
- int min = colSel.getMin();\r
- viewport.getAlignment().trimLeft(min);\r
- colSel.compensateForEdit(0, min);\r
-\r
- if (viewport.getSelectionGroup() != null)\r
- {\r
- viewport.getSelectionGroup().adjustForRemoveLeft(min);\r
- }\r
-\r
- Vector groups = viewport.alignment.getGroups();\r
- for (int i = 0; i < groups.size(); i++)\r
- {\r
- SequenceGroup sg = (SequenceGroup) groups.elementAt(i);\r
- if (!sg.adjustForRemoveLeft(min))\r
- {\r
- viewport.alignment.deleteGroup(sg);\r
- }\r
- }\r
- viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());\r
- }\r
- }\r
-\r
- public void remove2RightMenuItem_actionPerformed()\r
- {\r
- ColumnSelection colSel = viewport.getColumnSelection();\r
- if (colSel.size() > 0)\r
- {\r
- addHistoryItem(new HistoryItem("Remove Right", viewport.alignment,\r
- HistoryItem.HIDE));\r
- int max = colSel.getMax();\r
- viewport.getAlignment().trimRight(max);\r
- if (viewport.getSelectionGroup() != null)\r
- {\r
- viewport.getSelectionGroup().adjustForRemoveRight(max);\r
- }\r
-\r
- Vector groups = viewport.alignment.getGroups();\r
- for (int i = 0; i < groups.size(); i++)\r
- {\r
- SequenceGroup sg = (SequenceGroup) groups.elementAt(i);\r
- if (!sg.adjustForRemoveRight(max))\r
- {\r
- viewport.alignment.deleteGroup(sg);\r
- }\r
- }\r
- viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());\r
- }\r
-\r
- }\r
-\r
- public void removeGappedColumnMenuItem_actionPerformed()\r
- {\r
- addHistoryItem(new HistoryItem("Remove Gapped Columns",\r
- viewport.alignment,\r
- HistoryItem.HIDE));\r
-\r
- //This is to maintain viewport position on first residue\r
- //of first sequence\r
- SequenceI seq = viewport.alignment.getSequenceAt(0);\r
- int startRes = seq.findPosition(viewport.startRes);\r
-\r
- viewport.getAlignment().removeGaps();\r
-\r
- viewport.setStartRes(seq.findIndex(startRes)-1);\r
-\r
- viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());\r
- }\r
-\r
- public void removeAllGapsMenuItem_actionPerformed()\r
- {\r
- addHistoryItem(new HistoryItem("Remove Gaps", viewport.alignment,\r
- HistoryItem.HIDE));\r
-\r
- //This is to maintain viewport position on first residue\r
- //of first sequence\r
- SequenceI seq = viewport.alignment.getSequenceAt(0);\r
- int startRes = seq.findPosition(viewport.startRes);\r
-\r
- SequenceI current;\r
- int jSize;\r
-\r
- Vector seqs=null;\r
-\r
- int start=0, end = viewport.alignment.getWidth();\r
-\r
- if (viewport.getSelectionGroup() != null\r
- && viewport.getSelectionGroup().getSequences(false) != null\r
- && viewport.getSelectionGroup().getSize(false)>0)\r
- {\r
- seqs = viewport.getSelectionGroup().getSequences(true);\r
- start = viewport.getSelectionGroup().getStartRes();\r
- end = viewport.getSelectionGroup().getEndRes()+1;\r
- }\r
- else\r
- seqs = viewport.alignment.getSequences();\r
-\r
- for (int i = 0; i < seqs.size(); i++)\r
- {\r
- current = (SequenceI) seqs.elementAt(i);\r
- jSize = current.getLength();\r
-\r
- // Removing a range is much quicker than removing gaps\r
- // one by one for long sequences\r
- int j = start;\r
- int rangeStart=-1, rangeEnd=-1;\r
-\r
- do\r
- {\r
- if (jalview.util.Comparison.isGap(current.getCharAt(j)))\r
- {\r
- if(rangeStart==-1)\r
- {\r
- rangeStart = j;\r
- rangeEnd = j+1;\r
- }\r
- else\r
- {\r
- rangeEnd++;\r
- }\r
- j++;\r
- }\r
- else\r
- {\r
- if(rangeStart>-1)\r
- {\r
- current.deleteChars(rangeStart, rangeEnd);\r
- j-=rangeEnd-rangeStart;\r
- jSize-=rangeEnd-rangeStart;\r
- rangeStart = -1;\r
- rangeEnd = -1;\r
- }\r
- else\r
- j++;\r
- }\r
- }\r
- while (j < end && j < jSize);\r
- if(rangeStart>-1)\r
- {\r
- current.deleteChars(rangeStart, rangeEnd);\r
- }\r
- }\r
- viewport.setStartRes(seq.findIndex(startRes)-1);\r
- viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());\r
- }\r
-\r
- public void alignmentChanged()\r
- {\r
- viewport.alignment.padGaps();\r
- if(viewport.autocalculateConsensus)\r
- {\r
- viewport.updateConsensus();\r
- viewport.updateConservation();\r
- }\r
-\r
- resetAllColourSchemes();\r
- if(alignPanel.overviewPanel!=null)\r
- alignPanel.overviewPanel.updateOverviewImage();\r
-\r
- viewport.alignment.adjustSequenceAnnotations();\r
- alignPanel.repaint();\r
- }\r
-\r
- void resetAllColourSchemes()\r
- {\r
- ColourSchemeI cs = viewport.globalColourScheme;\r
- if(cs!=null)\r
- {\r
- if (cs instanceof ClustalxColourScheme)\r
- {\r
- ( (ClustalxColourScheme) viewport.getGlobalColourScheme()).\r
- resetClustalX(viewport.alignment.getSequences(),\r
- viewport.alignment.getWidth());\r
- }\r
-\r
- cs.setConsensus(viewport.vconsensus);\r
- if (cs.conservationApplied())\r
- {\r
- Alignment al = (Alignment) viewport.alignment;\r
- Conservation c = new Conservation("All",\r
- ResidueProperties.propHash, 3,\r
- al.getSequences(), 0,\r
- al.getWidth() - 1);\r
- c.calculate();\r
- c.verdict(false, viewport.ConsPercGaps);\r
-\r
- cs.setConservation(c);\r
- }\r
- }\r
-\r
- int s, sSize = viewport.alignment.getGroups().size();\r
- for(s=0; s<sSize; s++)\r
- {\r
- SequenceGroup sg = (SequenceGroup)viewport.alignment.getGroups().elementAt(s);\r
- if(sg.cs!=null && sg.cs instanceof ClustalxColourScheme)\r
- {\r
- ((ClustalxColourScheme)sg.cs).resetClustalX(\r
- sg.getSequences(true), sg.getWidth());\r
- }\r
- sg.recalcConservation();\r
- }\r
- }\r
-\r
-\r
-\r
- public void findMenuItem_actionPerformed()\r
- {\r
- new Finder(alignPanel);\r
- }\r
-\r
- public void font_actionPerformed()\r
- {\r
- new FontChooser(alignPanel);\r
- }\r
-\r
-\r
- public void seqLimits_itemStateChanged()\r
- {\r
- viewport.setShowJVSuffix(seqLimits.getState());\r
- alignPanel.fontChanged();\r
- alignPanel.repaint();\r
- }\r
-\r
-\r
- protected void colourTextMenuItem_actionPerformed()\r
- {\r
- viewport.setColourText(colourTextMenuItem.getState());\r
- alignPanel.repaint();\r
- }\r
-\r
- protected void wrapMenuItem_actionPerformed()\r
- {\r
- viewport.setWrapAlignment(wrapMenuItem.getState());\r
- alignPanel.setWrapAlignment(wrapMenuItem.getState());\r
- scaleAbove.setEnabled(wrapMenuItem.getState());\r
- scaleLeft.setEnabled(wrapMenuItem.getState());\r
- scaleRight.setEnabled(wrapMenuItem.getState());\r
- alignPanel.repaint();\r
- }\r
-\r
- protected void scaleAbove_actionPerformed()\r
- {\r
- viewport.setScaleAboveWrapped(scaleAbove.getState());\r
- alignPanel.repaint();\r
- }\r
-\r
- protected void scaleLeft_actionPerformed()\r
- {\r
- viewport.setScaleLeftWrapped(scaleLeft.getState());\r
- alignPanel.repaint();\r
- }\r
-\r
- protected void scaleRight_actionPerformed()\r
- {\r
- viewport.setScaleRightWrapped(scaleRight.getState());\r
- alignPanel.repaint();\r
- }\r
-\r
- public void viewBoxesMenuItem_actionPerformed()\r
- {\r
- viewport.setShowBoxes(viewBoxesMenuItem.getState());\r
- alignPanel.repaint();\r
- }\r
-\r
- public void viewTextMenuItem_actionPerformed()\r
- {\r
- viewport.setShowText(viewTextMenuItem.getState());\r
- alignPanel.repaint();\r
- }\r
-\r
- protected void renderGapsMenuItem_actionPerformed()\r
- {\r
- viewport.setRenderGaps(renderGapsMenuItem.getState());\r
- alignPanel.repaint();\r
- }\r
-\r
- public void annotationPanelMenuItem_actionPerformed()\r
- {\r
- viewport.setShowAnnotation(annotationPanelMenuItem.getState());\r
- alignPanel.setAnnotationVisible(annotationPanelMenuItem.getState());\r
- }\r
-\r
- public void featureSettings_actionPerformed()\r
- {\r
- new FeatureSettings(viewport, alignPanel);\r
- }\r
-\r
- public void overviewMenuItem_actionPerformed()\r
- {\r
- if (alignPanel.overviewPanel != null)\r
- {\r
- return;\r
- }\r
-\r
- Frame frame = new Frame();\r
- OverviewPanel overview = new OverviewPanel(alignPanel);\r
- frame.add(overview);\r
- // +50 must allow for applet frame window\r
- jalview.bin.JalviewLite.addFrame(frame, "Overview " + this.getTitle(),\r
- overview.preferredSize().width,\r
- overview.preferredSize().height + 50);\r
-\r
- frame.pack();\r
- frame.addWindowListener(new WindowAdapter()\r
- {\r
- public void windowClosing(WindowEvent e)\r
- {\r
- alignPanel.setOverviewPanel(null);\r
- };\r
- });\r
-\r
- alignPanel.setOverviewPanel(overview);\r
-\r
- }\r
-\r
- protected void noColourmenuItem_actionPerformed()\r
- {\r
- changeColour(null);\r
- }\r
-\r
- public void clustalColour_actionPerformed()\r
- {\r
- abovePIDThreshold.setState(false);\r
- changeColour(new ClustalxColourScheme(viewport.alignment.getSequences(),\r
- viewport.alignment.getWidth()));\r
- }\r
-\r
- public void zappoColour_actionPerformed()\r
- {\r
- changeColour(new ZappoColourScheme());\r
- }\r
-\r
- public void taylorColour_actionPerformed()\r
- {\r
- changeColour(new TaylorColourScheme());\r
- }\r
-\r
- public void hydrophobicityColour_actionPerformed()\r
- {\r
- changeColour(new HydrophobicColourScheme());\r
- }\r
-\r
- public void helixColour_actionPerformed()\r
- {\r
- changeColour(new HelixColourScheme());\r
- }\r
-\r
- public void strandColour_actionPerformed()\r
- {\r
- changeColour(new StrandColourScheme());\r
- }\r
-\r
- public void turnColour_actionPerformed()\r
- {\r
- changeColour(new TurnColourScheme());\r
- }\r
-\r
- public void buriedColour_actionPerformed()\r
- {\r
- changeColour(new BuriedColourScheme());\r
- }\r
-\r
- public void nucleotideColour_actionPerformed()\r
- {\r
- changeColour(new NucleotideColourScheme());\r
- }\r
-\r
- protected void applyToAllGroups_actionPerformed()\r
- {\r
- viewport.setColourAppliesToAllGroups(applyToAllGroups.getState());\r
- }\r
-\r
- void changeColour(ColourSchemeI cs)\r
- {\r
- int threshold = 0;\r
-\r
- if(cs!=null)\r
- {\r
- if (viewport.getAbovePIDThreshold())\r
- {\r
- threshold = SliderPanel.setPIDSliderSource(alignPanel, cs, "Background");\r
-\r
- cs.setThreshold(threshold, viewport.getIgnoreGapsConsensus());\r
-\r
- viewport.setGlobalColourScheme(cs);\r
- }\r
- else\r
- {\r
- cs.setThreshold(0, viewport.getIgnoreGapsConsensus());\r
- }\r
-\r
- if (viewport.getConservationSelected())\r
- {\r
-\r
- Alignment al = (Alignment) viewport.alignment;\r
- Conservation c = new Conservation("All",\r
- ResidueProperties.propHash, 3,\r
- al.getSequences(), 0,\r
- al.getWidth() - 1);\r
-\r
- c.calculate();\r
- c.verdict(false, viewport.ConsPercGaps);\r
-\r
- cs.setConservation(c);\r
-\r
- cs.setConservationInc(SliderPanel.setConservationSlider(alignPanel, cs,\r
- "Background"));\r
-\r
- }\r
- else\r
- {\r
- cs.setConservation(null);\r
- }\r
-\r
- cs.setConsensus(viewport.vconsensus);\r
-\r
- }\r
- viewport.setGlobalColourScheme(cs);\r
-\r
- if (viewport.getColourAppliesToAllGroups())\r
- {\r
- Vector groups = viewport.alignment.getGroups();\r
- for (int i = 0; i < groups.size(); i++)\r
- {\r
- SequenceGroup sg = (SequenceGroup) groups.elementAt(i);\r
-\r
- if(cs==null)\r
- {\r
- sg.cs = null;\r
- continue;\r
- }\r
- if (cs instanceof ClustalxColourScheme)\r
- {\r
- sg.cs = new ClustalxColourScheme(sg.getSequences(true), sg.getWidth());\r
- }\r
- else\r
- {\r
- try\r
- {\r
- sg.cs = (ColourSchemeI) cs.getClass().newInstance();\r
- }\r
- catch (Exception ex)\r
- {\r
- ex.printStackTrace();\r
- sg.cs = cs;\r
- }\r
- }\r
-\r
- if (viewport.getAbovePIDThreshold()\r
- || cs instanceof PIDColourScheme\r
- || cs instanceof Blosum62ColourScheme)\r
- {\r
- sg.cs.setThreshold(threshold, viewport.getIgnoreGapsConsensus());\r
- sg.cs.setConsensus(AAFrequency.calculate(sg.getSequences(true), 0, sg.getWidth()));\r
- }\r
- else\r
- sg.cs.setThreshold(0, viewport.getIgnoreGapsConsensus());\r
-\r
- if (viewport.getConservationSelected())\r
- {\r
- Conservation c = new Conservation("Group",\r
- ResidueProperties.propHash, 3,\r
- sg.getSequences(true), 0,\r
- viewport.alignment.getWidth() - 1);\r
- c.calculate();\r
- c.verdict(false, viewport.ConsPercGaps);\r
- sg.cs.setConservation(c);\r
- }\r
- else\r
- {\r
- sg.cs.setConservation(null);\r
- sg.cs.setThreshold(0, viewport.getIgnoreGapsConsensus());\r
- }\r
-\r
- }\r
- }\r
-\r
-\r
- if (alignPanel.getOverviewPanel() != null)\r
- {\r
- alignPanel.getOverviewPanel().updateOverviewImage();\r
- }\r
-\r
- alignPanel.repaint();\r
- }\r
-\r
-\r
-\r
- protected void modifyPID_actionPerformed()\r
- {\r
- if (viewport.getAbovePIDThreshold() && viewport.globalColourScheme!=null)\r
- {\r
- SliderPanel.setPIDSliderSource(alignPanel, viewport.getGlobalColourScheme(),\r
- "Background");\r
- SliderPanel.showPIDSlider();\r
- }\r
- }\r
-\r
- protected void modifyConservation_actionPerformed()\r
- {\r
- if (viewport.getConservationSelected() && viewport.globalColourScheme!=null)\r
- {\r
- SliderPanel.setConservationSlider(alignPanel, viewport.globalColourScheme,\r
- "Background");\r
- SliderPanel.showConservationSlider();\r
- }\r
- }\r
-\r
- protected void conservationMenuItem_actionPerformed()\r
- {\r
- viewport.setConservationSelected(conservationMenuItem.getState());\r
-\r
- viewport.setAbovePIDThreshold(false);\r
- abovePIDThreshold.setState(false);\r
-\r
- changeColour(viewport.getGlobalColourScheme());\r
-\r
- modifyConservation_actionPerformed();\r
- }\r
-\r
- public void abovePIDThreshold_actionPerformed()\r
- {\r
- viewport.setAbovePIDThreshold(abovePIDThreshold.getState());\r
-\r
- conservationMenuItem.setState(false);\r
- viewport.setConservationSelected(false);\r
-\r
- changeColour(viewport.getGlobalColourScheme());\r
-\r
- modifyPID_actionPerformed();\r
- }\r
-\r
- public void userDefinedColour_actionPerformed()\r
- {\r
- new UserDefinedColours(alignPanel, null);\r
- }\r
-\r
- public void PIDColour_actionPerformed()\r
- {\r
- changeColour(new PIDColourScheme());\r
- }\r
-\r
- public void BLOSUM62Colour_actionPerformed()\r
- {\r
- changeColour(new Blosum62ColourScheme());\r
- }\r
-\r
- public void sortPairwiseMenuItem_actionPerformed()\r
- {\r
- addHistoryItem(new HistoryItem("Pairwise Sort", viewport.alignment,\r
- HistoryItem.SORT));\r
- AlignmentSorter.sortByPID(viewport.getAlignment(),\r
- viewport.getAlignment().getSequenceAt(0));\r
- alignPanel.repaint();\r
- }\r
-\r
- public void sortIDMenuItem_actionPerformed()\r
- {\r
- addHistoryItem(new HistoryItem("ID Sort", viewport.alignment,\r
- HistoryItem.SORT));\r
- AlignmentSorter.sortByID(viewport.getAlignment());\r
- alignPanel.repaint();\r
- }\r
-\r
- public void sortGroupMenuItem_actionPerformed()\r
- {\r
- addHistoryItem(new HistoryItem("Group Sort", viewport.alignment,\r
- HistoryItem.SORT));\r
- AlignmentSorter.sortByGroup(viewport.getAlignment());\r
- alignPanel.repaint();\r
-\r
- }\r
-\r
- public void removeRedundancyMenuItem_actionPerformed()\r
- {\r
- new RedundancyPanel(alignPanel);\r
- }\r
-\r
- public void pairwiseAlignmentMenuItem_actionPerformed()\r
- {\r
- if (viewport.getSelectionGroup().getSize(false) > 1)\r
- {\r
- Frame frame = new Frame();\r
- frame.add(new PairwiseAlignPanel(alignPanel));\r
- jalview.bin.JalviewLite.addFrame(frame, "Pairwise Alignment", 600, 500);\r
- }\r
- }\r
-\r
- public void PCAMenuItem_actionPerformed()\r
- {\r
- //are the sequences aligned?\r
- if (!viewport.alignment.isAligned())\r
- {\r
- SequenceI current;\r
- int Width = viewport.getAlignment().getWidth();\r
-\r
- for (int i = 0; i < viewport.getAlignment().getSequences().size();\r
- i++)\r
- {\r
- current = viewport.getAlignment().getSequenceAt(i);\r
-\r
- if (current.getLength() < Width)\r
- {\r
- current.insertCharAt(Width - 1, viewport.getGapCharacter());\r
- }\r
- }\r
- alignPanel.repaint();\r
- }\r
-\r
- if ( (viewport.getSelectionGroup() != null &&\r
- viewport.getSelectionGroup().getSize(false) < 4 &&\r
- viewport.getSelectionGroup().getSize(false) > 0)\r
- || viewport.getAlignment().getHeight() < 4)\r
- {\r
- return;\r
- }\r
-\r
- try\r
- {\r
- new PCAPanel(viewport);\r
- }\r
- catch (java.lang.OutOfMemoryError ex)\r
- {\r
- }\r
-\r
- }\r
-\r
- public void averageDistanceTreeMenuItem_actionPerformed()\r
- {\r
- NewTreePanel("AV", "PID", "Average distance tree using PID");\r
- }\r
-\r
- public void neighbourTreeMenuItem_actionPerformed()\r
- {\r
- NewTreePanel("NJ", "PID", "Neighbour joining tree using PID");\r
- }\r
-\r
- protected void njTreeBlosumMenuItem_actionPerformed()\r
- {\r
- NewTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");\r
- }\r
-\r
- protected void avTreeBlosumMenuItem_actionPerformed()\r
- {\r
- NewTreePanel("AV", "BL", "Average distance tree using BLOSUM62PID");\r
- }\r
-\r
- void NewTreePanel(String type, String pwType, String title)\r
- {\r
- //are the sequences aligned?\r
- if (!viewport.alignment.isAligned())\r
- {\r
- SequenceI current;\r
- int Width = viewport.getAlignment().getWidth();\r
-\r
- for (int i = 0; i < viewport.getAlignment().getSequences().size();\r
- i++)\r
- {\r
- current = viewport.getAlignment().getSequenceAt(i);\r
-\r
- if (current.getLength() < Width)\r
- {\r
- current.insertCharAt(Width - 1, viewport.getGapCharacter());\r
- }\r
- }\r
- alignPanel.repaint();\r
-\r
- }\r
-\r
- final TreePanel tp = new TreePanel(viewport,\r
- type,\r
- pwType);\r
-\r
- addTreeMenuItem(tp, title);\r
-\r
- jalview.bin.JalviewLite.addFrame(tp, title, 600, 500);\r
- }\r
-\r
- void loadTree_actionPerformed()\r
- {\r
- CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);\r
- cap.setText("Paste your Newick tree file here.");\r
- cap.treeImport = true;\r
- Frame frame = new Frame();\r
- frame.add(cap);\r
- jalview.bin.JalviewLite.addFrame(frame, "Paste Newick file ", 400, 300);\r
- }\r
-\r
- public void loadTree(jalview.io.NewickFile tree, String treeFile)\r
- {\r
- TreePanel tp = new TreePanel(viewport,\r
- treeFile,\r
- "From File - ",\r
- tree);\r
- jalview.bin.JalviewLite.addFrame(tp, treeFile, 600, 500);\r
- addTreeMenuItem(tp, treeFile);\r
- }\r
-\r
- void addTreeMenuItem(final TreePanel treePanel, String title)\r
- {\r
- final MenuItem item = new MenuItem(title);\r
- sortByTreeMenu.add(item);\r
- item.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent evt)\r
- {\r
- addHistoryItem(new HistoryItem("Sort", viewport.alignment,\r
- HistoryItem.SORT));\r
- AlignmentSorter.sortByTree(viewport.getAlignment(), treePanel.getTree());\r
- alignPanel.repaint();\r
- }\r
- });\r
-\r
- treePanel.addWindowListener(new WindowAdapter()\r
- {\r
- public void windowClosing(WindowEvent e)\r
- {\r
- sortByTreeMenu.remove(item);\r
- };\r
- });\r
- }\r
-\r
- protected void documentation_actionPerformed()\r
- {\r
- showURL("http://www.jalview.org/help.html", "HELP");\r
- }\r
-\r
- protected void about_actionPerformed()\r
- {\r
-\r
- class AboutPanel extends Canvas\r
- {\r
- String version;\r
- public AboutPanel(String version)\r
- { this.version = version; }\r
-\r
- public void paint(Graphics g)\r
- {\r
- g.setColor(Color.white);\r
- g.fillRect(0, 0, getSize().width, getSize().height);\r
- g.setFont(new Font("Helvetica", Font.PLAIN, 12));\r
- FontMetrics fm = g.getFontMetrics();\r
- int fh = fm.getHeight();\r
- int y = 5, x = 7;\r
- g.setColor(Color.black);\r
- g.setFont(new Font("Helvetica", Font.BOLD, 14));\r
- g.drawString("Jalview - Release "+version, 200, y += fh);\r
- g.setFont(new Font("Helvetica", Font.PLAIN, 12));\r
- g.drawString("Authors: Michele Clamp, James Cuff, Steve Searle, Andrew Waterhouse, Jim Procter & Geoff Barton.",\r
- x, y += fh * 2);\r
- g.drawString("Current development managed by Andrew Waterhouse; Barton Group, University of Dundee.",\r
- x, y += fh);\r
- g.drawString(\r
- "For any issues relating to Jalview, email help@jalview.org", x,\r
- y += fh);\r
- g.drawString("If you use JalView, please cite:", x, y += fh + 8);\r
- g.drawString("\"Clamp, M., Cuff, J., Searle, S. M. and Barton, G. J. (2004), The Jalview Java Alignment Editor\"",\r
- x, y += fh);\r
- g.drawString("Bioinformatics, 2004 20;426-7.", x, y += fh);\r
- }\r
- }\r
-\r
- String version = "test";\r
- java.net.URL url = getClass().getResource("/.build_properties");\r
- if (url != null)\r
- {\r
- try\r
- {\r
- BufferedReader reader = new BufferedReader(new InputStreamReader(\r
- url.openStream()));\r
- String line;\r
- while ( (line = reader.readLine()) != null)\r
- {\r
- if (line.indexOf("VERSION") > -1)\r
- {\r
- version = line.substring(line.indexOf("=") + 1);\r
- }\r
- }\r
- }\r
- catch (Exception ex)\r
- {\r
- ex.printStackTrace();\r
- }\r
- }\r
-\r
-\r
- Frame frame = new Frame();\r
- frame.add(new AboutPanel(version));\r
- jalview.bin.JalviewLite.addFrame(frame, "Jalview", 580, 200);\r
-\r
- }\r
-\r
- public void showURL(String url, String target)\r
- {\r
- if (viewport.applet == null)\r
- {\r
- System.out.println("Not running as applet - no browser available.");\r
- }\r
- else\r
- {\r
- try\r
- {\r
- System.out.println("Show url: "+url);\r
- viewport.applet.getAppletContext().showDocument(new java.net.URL(url),\r
- target);\r
- }\r
- catch (Exception ex)\r
- {\r
- ex.printStackTrace();\r
- }\r
- }\r
- }\r
-\r
-\r
- //////////////////////////////////////////////////////////////////////////////////\r
- //JBuilder Graphics here\r
-\r
- protected MenuBar alignFrameMenuBar = new MenuBar();\r
- protected Menu fileMenu = new Menu("File");\r
- protected MenuItem loadApplication = new MenuItem("View in Full Application");\r
- protected MenuItem loadTree = new MenuItem("Load Associated Tree");\r
- protected MenuItem closeMenuItem = new MenuItem("Close");\r
- protected Menu editMenu = new Menu("Edit");\r
- protected Menu viewMenu = new Menu("View");\r
- protected Menu colourMenu = new Menu("Colour");\r
- protected Menu calculateMenu = new Menu("Calculate");\r
- protected MenuItem selectAllSequenceMenuItem = new MenuItem("Select all");\r
- protected MenuItem deselectAllSequenceMenuItem = new MenuItem("Deselect All");\r
- protected MenuItem invertSequenceMenuItem = new MenuItem("Invert Selection");\r
- protected MenuItem remove2LeftMenuItem = new MenuItem();\r
- protected MenuItem remove2RightMenuItem = new MenuItem();\r
- protected MenuItem removeGappedColumnMenuItem = new MenuItem();\r
- protected MenuItem removeAllGapsMenuItem = new MenuItem();\r
- protected CheckboxMenuItem viewBoxesMenuItem = new CheckboxMenuItem();\r
- protected CheckboxMenuItem viewTextMenuItem = new CheckboxMenuItem();\r
- protected MenuItem sortPairwiseMenuItem = new MenuItem();\r
- protected MenuItem sortIDMenuItem = new MenuItem();\r
- protected MenuItem sortGroupMenuItem = new MenuItem();\r
- protected MenuItem removeRedundancyMenuItem = new MenuItem();\r
- protected MenuItem pairwiseAlignmentMenuItem = new MenuItem();\r
- protected MenuItem PCAMenuItem = new MenuItem();\r
- protected MenuItem averageDistanceTreeMenuItem = new MenuItem();\r
- protected MenuItem neighbourTreeMenuItem = new MenuItem();\r
- BorderLayout borderLayout1 = new BorderLayout();\r
- public Label statusBar = new Label();\r
- protected Menu outputTextboxMenu = new Menu();\r
- protected MenuItem clustalColour = new MenuItem();\r
- protected MenuItem zappoColour = new MenuItem();\r
- protected MenuItem taylorColour = new MenuItem();\r
- protected MenuItem hydrophobicityColour = new MenuItem();\r
- protected MenuItem helixColour = new MenuItem();\r
- protected MenuItem strandColour = new MenuItem();\r
- protected MenuItem turnColour = new MenuItem();\r
- protected MenuItem buriedColour = new MenuItem();\r
- protected MenuItem userDefinedColour = new MenuItem();\r
- protected MenuItem PIDColour = new MenuItem();\r
- protected MenuItem BLOSUM62Colour = new MenuItem();\r
- MenuItem njTreeBlosumMenuItem = new MenuItem();\r
- MenuItem avDistanceTreeBlosumMenuItem = new MenuItem();\r
- protected CheckboxMenuItem annotationPanelMenuItem = new CheckboxMenuItem();\r
- protected CheckboxMenuItem colourTextMenuItem = new CheckboxMenuItem();\r
- MenuItem overviewMenuItem = new MenuItem();\r
- protected MenuItem undoMenuItem = new MenuItem();\r
- protected MenuItem redoMenuItem = new MenuItem();\r
- protected CheckboxMenuItem conservationMenuItem = new CheckboxMenuItem();\r
- MenuItem noColourmenuItem = new MenuItem();\r
- protected CheckboxMenuItem wrapMenuItem = new CheckboxMenuItem();\r
- protected CheckboxMenuItem renderGapsMenuItem = new CheckboxMenuItem();\r
- MenuItem findMenuItem = new MenuItem();\r
- Menu searchMenu = new Menu();\r
- protected CheckboxMenuItem abovePIDThreshold = new CheckboxMenuItem();\r
- protected MenuItem nucleotideColour = new MenuItem();\r
- MenuItem deleteGroups = new MenuItem();\r
- MenuItem delete = new MenuItem();\r
- MenuItem copy = new MenuItem();\r
- MenuItem cut = new MenuItem();\r
- Menu pasteMenu = new Menu();\r
- MenuItem pasteNew = new MenuItem();\r
- MenuItem pasteThis = new MenuItem();\r
- protected CheckboxMenuItem applyToAllGroups = new CheckboxMenuItem();\r
- protected MenuItem font = new MenuItem();\r
- protected CheckboxMenuItem scaleAbove = new CheckboxMenuItem();\r
- protected CheckboxMenuItem scaleLeft = new CheckboxMenuItem();\r
- protected CheckboxMenuItem scaleRight = new CheckboxMenuItem();\r
- MenuItem modifyPID = new MenuItem();\r
- MenuItem modifyConservation = new MenuItem();\r
- protected CheckboxMenuItem autoCalculate\r
- = new CheckboxMenuItem("Autocalculate Consensus", true);\r
- protected Menu sortByTreeMenu = new Menu();\r
- Menu sort = new Menu();\r
- Menu calculate = new Menu();\r
- MenuItem inputText = new MenuItem();\r
- Menu helpMenu = new Menu();\r
- MenuItem documentation = new MenuItem();\r
- MenuItem about = new MenuItem();\r
- protected CheckboxMenuItem seqLimits = new CheckboxMenuItem();\r
- Panel embeddedMenu;\r
- Label embeddedEdit;\r
- Label embeddedSearch;\r
- Label embeddedView;\r
- Label embeddedColour;\r
- Label embeddedFile;\r
- Label embeddedHelp;\r
- Label embeddedCalculate;\r
- FlowLayout flowLayout1;\r
-\r
- private void jbInit() throws Exception {\r
-\r
- setMenuBar(alignFrameMenuBar);\r
-\r
- MenuItem item;\r
-\r
- // dynamically fill save as menu with available formats\r
- for (int i = 0; i < jalview.io.AppletFormatAdapter.formats.size(); i++)\r
- {\r
-\r
- item = new MenuItem( (String) jalview.io.AppletFormatAdapter.formats.\r
- elementAt(\r
- i));\r
- item.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- outputText_actionPerformed(e);\r
- }\r
- });\r
-\r
- outputTextboxMenu.add(item);\r
- }\r
- closeMenuItem.addActionListener(this);\r
- loadApplication.addActionListener(this);\r
-\r
- loadTree.addActionListener(this);\r
- selectAllSequenceMenuItem.addActionListener(this);\r
- deselectAllSequenceMenuItem.addActionListener(this);\r
- invertSequenceMenuItem.addActionListener(this);\r
- remove2LeftMenuItem.setLabel("Remove Left");\r
- remove2LeftMenuItem.addActionListener(this);\r
- remove2RightMenuItem.setLabel("Remove Right");\r
- remove2RightMenuItem.addActionListener(this);\r
- removeGappedColumnMenuItem.setLabel("Remove Empty Columns");\r
- removeGappedColumnMenuItem.addActionListener(this);\r
- removeAllGapsMenuItem.setLabel("Remove All Gaps");\r
- removeAllGapsMenuItem.addActionListener(this);\r
- viewBoxesMenuItem.setLabel("Boxes");\r
- viewBoxesMenuItem.setState(true);\r
- viewBoxesMenuItem.addItemListener(this);\r
- viewTextMenuItem.setLabel("Text");\r
- viewTextMenuItem.setState(true);\r
- viewTextMenuItem.addItemListener(this);\r
- sortPairwiseMenuItem.setLabel("by Pairwise Identity");\r
- sortPairwiseMenuItem.addActionListener(this);\r
- sortIDMenuItem.setLabel("by ID");\r
- sortIDMenuItem.addActionListener(this);\r
- sortGroupMenuItem.setLabel("by Group");\r
- sortGroupMenuItem.addActionListener(this);\r
- removeRedundancyMenuItem.setLabel("Remove Redundancy...");\r
- removeRedundancyMenuItem.addActionListener(this);\r
- pairwiseAlignmentMenuItem.setLabel("Pairwise Alignments...");\r
- pairwiseAlignmentMenuItem.addActionListener(this);\r
- PCAMenuItem.setLabel("Principal Component Analysis");\r
- PCAMenuItem.addActionListener(this);\r
- averageDistanceTreeMenuItem.setLabel(\r
- "Average Distance Using % Identity");\r
- averageDistanceTreeMenuItem.addActionListener(this);\r
- neighbourTreeMenuItem.setLabel("Neighbour Joining Using % Identity");\r
- neighbourTreeMenuItem.addActionListener(this);\r
- alignFrameMenuBar.setFont(new java.awt.Font("Verdana", 0, 11));\r
- statusBar.setBackground(Color.white);\r
- statusBar.setFont(new java.awt.Font("Verdana", 0, 11));\r
- statusBar.setText("Status bar");\r
- outputTextboxMenu.setLabel("Output to Textbox");\r
- clustalColour.setLabel("Clustalx");\r
-\r
- clustalColour.addActionListener(this);\r
- zappoColour.setLabel("Zappo");\r
- zappoColour.addActionListener(this);\r
- taylorColour.setLabel("Taylor");\r
- taylorColour.addActionListener(this);\r
- hydrophobicityColour.setLabel("Hydrophobicity");\r
- hydrophobicityColour.addActionListener(this);\r
- helixColour.setLabel("Helix Propensity");\r
- helixColour.addActionListener(this);\r
- strandColour.setLabel("Strand Propensity");\r
- strandColour.addActionListener(this);\r
- turnColour.setLabel("Turn Propensity");\r
- turnColour.addActionListener(this);\r
- buriedColour.setLabel("Buried Index");\r
- buriedColour.addActionListener(this);\r
- userDefinedColour.setLabel("User Defined...");\r
- userDefinedColour.addActionListener(this);\r
- PIDColour.setLabel("Percentage Identity");\r
- PIDColour.addActionListener(this);\r
- BLOSUM62Colour.setLabel("BLOSUM62 Score");\r
- BLOSUM62Colour.addActionListener(this);\r
- avDistanceTreeBlosumMenuItem.setLabel(\r
- "Average Distance Using BLOSUM62");\r
- avDistanceTreeBlosumMenuItem.addActionListener(this);\r
- njTreeBlosumMenuItem.setLabel("Neighbour Joining Using BLOSUM62");\r
- njTreeBlosumMenuItem.addActionListener(this);\r
- annotationPanelMenuItem.setLabel("Show Annotations");\r
- annotationPanelMenuItem.addItemListener(this);\r
- colourTextMenuItem.setLabel("Colour Text");\r
- colourTextMenuItem.addItemListener(this);\r
- overviewMenuItem.setLabel("Overview Window");\r
- overviewMenuItem.addActionListener(this);\r
- undoMenuItem.setEnabled(false);\r
- undoMenuItem.setLabel("Undo");\r
- undoMenuItem.addActionListener(this);\r
- redoMenuItem.setEnabled(false);\r
- redoMenuItem.setLabel("Redo");\r
- redoMenuItem.addActionListener(this);\r
- conservationMenuItem.setLabel("by Conservation");\r
- conservationMenuItem.addItemListener(this);\r
- noColourmenuItem.setLabel("None");\r
- noColourmenuItem.addActionListener(this);\r
- wrapMenuItem.setLabel("Wrap");\r
- wrapMenuItem.addItemListener(this);\r
- renderGapsMenuItem.setLabel("Show Gaps");\r
- renderGapsMenuItem.setState(true);\r
- renderGapsMenuItem.addItemListener(this);\r
- findMenuItem.setLabel("Find...");\r
- findMenuItem.addActionListener(this);\r
- searchMenu.setLabel("Search");\r
-\r
- abovePIDThreshold.setLabel("Above Identity Threshold");\r
- abovePIDThreshold.addItemListener(this);\r
- nucleotideColour.setLabel("Nucleotide");\r
- nucleotideColour.addActionListener(this);\r
- deleteGroups.setLabel("Undefine Groups");\r
- deleteGroups.addActionListener(this);\r
- copy.setLabel("Copy");\r
- copy.addActionListener(this);\r
- cut.setLabel("Cut");\r
- cut.addActionListener(this);\r
- delete.setLabel("Delete");\r
- delete.addActionListener(this);\r
- pasteMenu.setLabel("Paste");\r
- pasteNew.setLabel("To New Alignment");\r
- pasteNew.addActionListener(this);\r
- pasteThis.setLabel("Add To This Alignment");\r
- pasteThis.addActionListener(this);\r
- applyToAllGroups.setLabel("Apply Colour To All Groups");\r
- applyToAllGroups.setState(true);\r
- applyToAllGroups.addItemListener(this);\r
- font.setLabel("Font...");\r
- font.addActionListener(this);\r
- scaleAbove.setLabel("Scale Above");\r
- scaleAbove.setState(true);\r
- scaleAbove.setEnabled(false);\r
- scaleAbove.addItemListener(this);\r
- scaleLeft.setEnabled(false);\r
- scaleLeft.setState(true);\r
- scaleLeft.setLabel("Scale Left");\r
- scaleLeft.addItemListener(this);\r
- scaleRight.setEnabled(false);\r
- scaleRight.setState(true);\r
- scaleRight.setLabel("Scale Right");\r
- scaleRight.addItemListener(this);\r
- modifyPID.setLabel("Modify Identity Threshold...");\r
- modifyPID.addActionListener(this);\r
- modifyConservation.setLabel("Modify Conservation Threshold...");\r
- modifyConservation.addActionListener(this);\r
- sortByTreeMenu.setLabel("By Tree Order");\r
- sort.setLabel("Sort");\r
- calculate.setLabel("Calculate Tree");\r
- autoCalculate.addItemListener(this);\r
- inputText.setLabel("Input from textbox");\r
- inputText.addActionListener(this);\r
-\r
- helpMenu.setLabel("Help");\r
- documentation.setLabel("Documentation");\r
- documentation.addActionListener(this);\r
-\r
- about.setLabel("About...");\r
- about.addActionListener(this);\r
- seqLimits.setState(true);\r
- seqLimits.setLabel("Show Sequence Limits");\r
- seqLimits.addItemListener(this);\r
- featureSettings.setLabel("Feature Settings...");\r
- featureSettings.addActionListener(this);\r
- sequenceFeatures.setLabel("Sequence Features");\r
- sequenceFeatures.addItemListener(this);\r
- sequenceFeatures.setState(false);\r
- annotationColour.setLabel("by Annotation...");\r
- annotationColour.addActionListener(this);\r
-\r
- alignFrameMenuBar.add(fileMenu);\r
- alignFrameMenuBar.add(editMenu);\r
- alignFrameMenuBar.add(searchMenu);\r
- alignFrameMenuBar.add(viewMenu);\r
- alignFrameMenuBar.add(colourMenu);\r
- alignFrameMenuBar.add(calculateMenu);\r
- alignFrameMenuBar.add(helpMenu);\r
- fileMenu.add(inputText);\r
- fileMenu.add(outputTextboxMenu);\r
- if(jalviewServletURL!=null)\r
- fileMenu.add(loadApplication);\r
- fileMenu.addSeparator();\r
- fileMenu.add(loadTree);\r
- fileMenu.add(closeMenuItem);\r
- editMenu.add(undoMenuItem);\r
- editMenu.add(redoMenuItem);\r
- editMenu.add(cut);\r
- editMenu.add(copy);\r
- editMenu.add(pasteMenu);\r
- editMenu.add(delete);\r
- editMenu.addSeparator();\r
- editMenu.add(selectAllSequenceMenuItem);\r
- editMenu.add(deselectAllSequenceMenuItem);\r
- editMenu.add(invertSequenceMenuItem);\r
- editMenu.add(deleteGroups);\r
- editMenu.addSeparator();\r
- editMenu.add(remove2LeftMenuItem);\r
- editMenu.add(remove2RightMenuItem);\r
- editMenu.add(removeGappedColumnMenuItem);\r
- editMenu.add(removeAllGapsMenuItem);\r
- editMenu.add(removeRedundancyMenuItem);\r
- searchMenu.add(findMenuItem);\r
- viewMenu.add(font);\r
- viewMenu.addSeparator();\r
- viewMenu.add(seqLimits);\r
- viewMenu.addSeparator();\r
- viewMenu.add(wrapMenuItem);\r
- viewMenu.add(scaleAbove);\r
- viewMenu.add(scaleLeft);\r
- viewMenu.add(scaleRight);\r
- viewMenu.addSeparator();\r
- viewMenu.add(viewBoxesMenuItem);\r
- viewMenu.add(viewTextMenuItem);\r
- viewMenu.add(colourTextMenuItem);\r
- viewMenu.add(renderGapsMenuItem);\r
- viewMenu.add(annotationPanelMenuItem);\r
- viewMenu.addSeparator();\r
- viewMenu.add(sequenceFeatures);\r
- viewMenu.add(featureSettings);\r
- viewMenu.addSeparator();\r
- viewMenu.add(overviewMenuItem);\r
- colourMenu.add(applyToAllGroups);\r
- colourMenu.addSeparator();\r
- colourMenu.add(noColourmenuItem);\r
- colourMenu.add(clustalColour);\r
- colourMenu.add(BLOSUM62Colour);\r
- colourMenu.add(PIDColour);\r
- colourMenu.add(zappoColour);\r
- colourMenu.add(taylorColour);\r
- colourMenu.add(hydrophobicityColour);\r
- colourMenu.add(helixColour);\r
- colourMenu.add(strandColour);\r
- colourMenu.add(turnColour);\r
- colourMenu.add(buriedColour);\r
- colourMenu.add(nucleotideColour);\r
- colourMenu.add(userDefinedColour);\r
- colourMenu.addSeparator();\r
- colourMenu.add(conservationMenuItem);\r
- colourMenu.add(modifyConservation);\r
- colourMenu.add(abovePIDThreshold);\r
- colourMenu.add(modifyPID);\r
- colourMenu.add(annotationColour);\r
- calculateMenu.add(sort);\r
- calculateMenu.add(calculate);\r
- calculateMenu.addSeparator();\r
- calculateMenu.add(pairwiseAlignmentMenuItem);\r
- calculateMenu.add(PCAMenuItem);\r
- calculateMenu.add(autoCalculate);\r
- this.add(statusBar, BorderLayout.SOUTH);\r
- pasteMenu.add(pasteNew);\r
- pasteMenu.add(pasteThis);\r
- sort.add(sortIDMenuItem);\r
- sort.add(sortByTreeMenu);\r
- sort.add(sortGroupMenuItem);\r
- sort.add(sortPairwiseMenuItem);\r
- calculate.add(averageDistanceTreeMenuItem);\r
- calculate.add(neighbourTreeMenuItem);\r
- calculate.add(avDistanceTreeBlosumMenuItem);\r
- calculate.add(njTreeBlosumMenuItem);\r
- helpMenu.add(documentation);\r
- helpMenu.add(about);\r
- }\r
-\r
- public void setEmbedded()\r
- {\r
-\r
- embeddedMenu = new Panel();\r
- embeddedEdit = new Label();\r
- embeddedSearch = new Label();\r
- embeddedView = new Label();\r
- embeddedColour = new Label();\r
- embeddedFile = new Label();\r
- embeddedHelp = new Label();\r
- embeddedCalculate = new Label();\r
- flowLayout1 = new FlowLayout();\r
- embeddedMenu.setBackground(Color.lightGray);\r
- embeddedMenu.setLayout(flowLayout1);\r
- embeddedEdit.setText("Edit");\r
- embeddedEdit.setFont(new java.awt.Font("Arial", Font.PLAIN, 10));\r
- embeddedSearch.setText("Search");\r
- embeddedSearch.setFont(new java.awt.Font("Arial", Font.PLAIN, 10));\r
- embeddedView.setText("View");\r
- embeddedView.setFont(new java.awt.Font("Arial", Font.PLAIN, 10));\r
- embeddedColour.setText("Colour");\r
- embeddedColour.setFont(new java.awt.Font("Arial", Font.PLAIN, 10));\r
- embeddedFile.setFont(new java.awt.Font("Arial", Font.PLAIN, 10));\r
- embeddedFile.setText("File");\r
- embeddedHelp.setFont(new java.awt.Font("Arial", Font.PLAIN, 10));\r
- embeddedHelp.setText("Help");\r
- embeddedCalculate.setFont(new java.awt.Font("Arial", Font.PLAIN, 10));\r
- embeddedCalculate.setText("Calculate");\r
- embeddedMenu.add(embeddedFile);\r
- embeddedMenu.add(embeddedEdit);\r
- embeddedMenu.add(embeddedSearch);\r
- embeddedMenu.add(embeddedView);\r
- embeddedMenu.add(embeddedColour);\r
- embeddedMenu.add(embeddedCalculate);\r
- embeddedMenu.add(embeddedHelp);\r
- flowLayout1.setAlignment(FlowLayout.LEFT);\r
- flowLayout1.setHgap(2);\r
- flowLayout1.setVgap(0);\r
- embeddedFile.addMouseListener(this);\r
- embeddedEdit.addMouseListener(this);\r
- embeddedSearch.addMouseListener(this);\r
- embeddedView.addMouseListener(this);\r
- embeddedColour.addMouseListener(this);\r
- embeddedCalculate.addMouseListener(this);\r
- embeddedHelp.addMouseListener(this);\r
-\r
- // setVisible(false);\r
- fileMenu.remove(closeMenuItem);\r
- fileMenu.remove(3); // Seperator\r
-\r
- viewport.applet.setLayout(new BorderLayout());\r
- viewport.applet.add(embeddedMenu, BorderLayout.NORTH);\r
- viewport.applet.add(statusBar, BorderLayout.SOUTH);\r
- // viewport.applet.validate();\r
-\r
- alignPanel.setSize(viewport.applet.size().width, viewport.applet.size().height\r
- - embeddedMenu.HEIGHT - statusBar.HEIGHT);\r
-\r
- viewport.applet.add(alignPanel, BorderLayout.CENTER);\r
- viewport.applet.validate();\r
-\r
- }\r
-\r
-\r
-\r
- PopupMenu filePopup, editPopup, searchPopup,\r
- viewPopup, colourPopup, calculatePopup, helpPopup;\r
- MenuItem featureSettings = new MenuItem();\r
- CheckboxMenuItem sequenceFeatures = new CheckboxMenuItem();\r
- MenuItem annotationColour = new MenuItem();\r
-\r
- public void mousePressed(MouseEvent evt)\r
- {\r
- PopupMenu popup = null;\r
- Label source = (Label)evt.getSource();\r
- if(source==embeddedFile)\r
- {\r
- popup = filePopup = genPopupMenu(filePopup, fileMenu);\r
- }\r
- else if(source==embeddedEdit)\r
- {\r
- popup = editPopup = genPopupMenu(editPopup, editMenu);\r
- }\r
- else if(source==embeddedSearch)\r
- {\r
- popup = searchPopup = genPopupMenu(searchPopup, searchMenu);\r
- }\r
- else if(source==embeddedView)\r
- {\r
- popup = viewPopup = genPopupMenu(viewPopup, viewMenu);\r
- }\r
- else if(source==embeddedColour)\r
- {\r
- popup = colourPopup = genPopupMenu(colourPopup, colourMenu);\r
- }\r
- else if(source==embeddedCalculate)\r
- {\r
- popup = calculatePopup = genPopupMenu(calculatePopup, calculateMenu);\r
- }\r
- else if(source==embeddedHelp)\r
- {\r
- popup = helpPopup = genPopupMenu(helpPopup, helpMenu);\r
- }\r
-\r
- embeddedMenu.add(popup);\r
- popup.show(embeddedMenu,\r
- source.getBounds().x,\r
- source.getBounds().y + source.getBounds().getSize().height);\r
- }\r
-\r
- PopupMenu genPopupMenu(PopupMenu popup, Menu original)\r
- {\r
- if(popup!=null)\r
- {\r
- return popup;\r
- }\r
- popup = new PopupMenu();\r
- int m, mSize = original.getItemCount();\r
- for(m=0; m<mSize; m++)\r
- {\r
- popup.add(original.getItem(m));\r
- mSize--;\r
- m--;\r
- }\r
-\r
- return popup;\r
- }\r
- public void mouseClicked(MouseEvent evt)\r
- {}\r
- public void mouseReleased(MouseEvent evt)\r
- {}\r
- public void mouseEntered(MouseEvent evt)\r
- {}\r
- public void mouseExited(MouseEvent evt)\r
- {}\r
-\r
-}\r
-\r
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
+ * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ */
+package jalview.appletgui;
+
+import java.io.*;
+import java.net.*;
+import java.util.*;
+
+import java.applet.Applet;
+import java.awt.*;
+import java.awt.event.*;
+
+import org.jmol.api.JmolViewer;
+
+import jalview.analysis.*;
+import jalview.api.SequenceStructureBinding;
+import jalview.bin.JalviewLite;
+import jalview.commands.*;
+import jalview.datamodel.*;
+import jalview.io.*;
+import jalview.schemes.*;
+
+public class AlignFrame extends EmbmenuFrame implements ActionListener,
+ ItemListener, KeyListener
+{
+ 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);
+ displayNonconservedMenuItem.setState(viewport.getShowunconserved());
+
+ 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();
+ }
+ else if (param.equalsIgnoreCase("Length"))
+ {
+ sortLengthMenuItem_actionPerformed();
+ }
+ }
+
+ param = applet.getParameter("wrap");
+ if (param != null)
+ {
+ if (param.equalsIgnoreCase("true"))
+ {
+ wrapMenuItem.setState(true);
+ wrapMenuItem_actionPerformed();
+ }
+ }
+ param = applet.getParameter("centrecolumnlabels");
+ if (param != null)
+ {
+ centreColumnLabelFlag.setState(true);
+ centreColumnLabelFlag_stateChanged();
+ }
+ 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);
+ createAlignFrameWindow(embedded, title);
+ 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);
+ if (viewport.featureSettings != null)
+ {
+ viewport.featureSettings.refreshTable();
+ }
+ 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();
+ toggleHiddenRegions(toggleSeqs, toggleCols);
+ 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())
+ {
+ invertColSel_actionPerformed();
+ }
+ else
+ {
+ invertSequenceMenuItem_actionPerformed();
+ }
+ }
+ break;
+
+ case KeyEvent.VK_U:
+ if (evt.isControlDown())
+ {
+ this.deleteGroups_actionPerformed();
+ }
+ break;
+
+ case KeyEvent.VK_T:
+ if (evt.isControlDown())
+ {
+ newView(null);
+ }
+ break;
+
+ }
+ alignPanel.paintAlignment(true);
+ }
+
+ /**
+ * called by key handler and the hide all/show all menu items
+ *
+ * @param toggleSeqs
+ * @param toggleCols
+ */
+ private void toggleHiddenRegions(boolean toggleSeqs, boolean toggleCols)
+ {
+ boolean hide = false;
+ SequenceGroup sg = viewport.getSelectionGroup();
+ if (!toggleSeqs && !toggleCols)
+ {
+ // Hide everything by the current selection - this is a hack - we do the
+ // invert and then hide
+ // first check that there will be visible columns after the invert.
+ if ((viewport.colSel != null && viewport.colSel.getSelected() != null && viewport.colSel
+ .getSelected().size() > 0)
+ || (sg != null && sg.getSize() > 0 && sg.getStartRes() <= sg
+ .getEndRes()))
+ {
+ // now invert the sequence set, if required - empty selection implies
+ // that no hiding is required.
+ if (sg != null)
+ {
+ invertSequenceMenuItem_actionPerformed();
+ sg = viewport.getSelectionGroup();
+ toggleSeqs = true;
+
+ }
+ viewport.expandColSelection(sg, true);
+ // finally invert the column selection and get the new sequence
+ // selection and indicate it should be hidden.
+ invertColSel_actionPerformed();
+ toggleCols = true;
+ }
+ }
+
+ 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();
+ }
+ }
+ }
+
+ public void keyReleased(KeyEvent evt)
+ {
+ }
+
+ public void keyTyped(KeyEvent evt)
+ {
+ }
+
+ public void itemStateChanged(ItemEvent evt)
+ {
+ if (evt.getSource() == displayNonconservedMenuItem)
+ {
+ displayNonconservedMenuItem_actionPerformed();
+ }
+ else 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();
+ }
+ else if (evt.getSource() == this.centreColumnLabelFlag)
+ {
+ centreColumnLabelFlag_stateChanged();
+ }
+ else if (evt.getSource() == this.followMouseOverFlag)
+ {
+ mouseOverFlag_stateChanged();
+ }
+
+ alignPanel.paintAlignment(true);
+ }
+
+ private void mouseOverFlag_stateChanged()
+ {
+ viewport.followHighlight = followMouseOverFlag.getState();
+ // TODO: could kick the scrollTo mechanism to reset view for current
+ // searchresults.
+ }
+
+ private void centreColumnLabelFlag_stateChanged()
+ {
+ viewport.centreColumnLabels = centreColumnLabelFlag.getState();
+ this.alignPanel.annotationPanel.repaint();
+ }
+
+ public void actionPerformed(ActionEvent evt)
+ {
+ Object source = evt.getSource();
+
+ if (source == inputText)
+ {
+ inputText_actionPerformed();
+ }
+ else if (source == loadTree)
+ {
+ loadTree_actionPerformed();
+ }
+ else if (source == loadApplication)
+ {
+ launchFullApplication();
+ }
+ else if (source == 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 == grpsFromSelection)
+ {
+ makeGrpsFromSelection_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(null);
+ }
+ else if (source == showColumns)
+ {
+ viewport.showAllHiddenColumns();
+ alignPanel.paintAlignment(true);
+ }
+ else if (source == showSeqs)
+ {
+ viewport.showAllHiddenSeqs();
+ alignPanel.paintAlignment(true);
+ }
+ else if (source == hideColumns)
+ {
+ viewport.hideSelectedColumns();
+ alignPanel.paintAlignment(true);
+ }
+ else if (source == hideSequences
+ && viewport.getSelectionGroup() != null)
+ {
+ viewport.hideAllSelectedSeqs();
+ alignPanel.paintAlignment(true);
+ }
+ else if (source == hideAllButSelection)
+ {
+ toggleHiddenRegions(false, false);
+ alignPanel.paintAlignment(true);
+ }
+ else if (source == hideAllSelection)
+ {
+ SequenceGroup sg = viewport.getSelectionGroup();
+ viewport.expandColSelection(sg, false);
+ viewport.hideAllSelectedSeqs();
+ viewport.hideSelectedColumns();
+ alignPanel.paintAlignment(true);
+ }
+ else if (source == showAllHidden)
+ {
+ viewport.showAllHiddenColumns();
+ viewport.showAllHiddenSeqs();
+ alignPanel.paintAlignment(true);
+ }
+ else if (source == featureSettings)
+ {
+ new FeatureSettings(alignPanel);
+ }
+ else if (source == alProperties)
+ {
+ StringBuffer contents = new StringBuffer();
+
+ float avg = 0;
+ int min = Integer.MAX_VALUE, max = 0;
+ for (int i = 0; i < viewport.alignment.getHeight(); i++)
+ {
+ int size = viewport.alignment.getSequenceAt(i).getEnd()
+ - viewport.alignment.getSequenceAt(i).getStart();
+ avg += size;
+ if (size > max)
+ max = size;
+ if (size < min)
+ min = size;
+ }
+ avg = avg / (float) viewport.alignment.getHeight();
+
+ contents.append("\nSequences: " + viewport.alignment.getHeight());
+ contents.append("\nMinimum Sequence Length: " + min);
+ contents.append("\nMaximum Sequence Length: " + max);
+ contents.append("\nAverage Length: " + (int) avg);
+
+ if (((Alignment) viewport.alignment).alignmentProperties != null)
+ {
+ Hashtable props = ((Alignment) viewport.alignment).alignmentProperties;
+ Enumeration en = props.keys();
+ while (en.hasMoreElements())
+ {
+ String key = en.nextElement().toString();
+ contents.append("\n" + key + "\t" + props.get(key));
+ }
+ }
+
+ CutAndPasteTransfer cap = new CutAndPasteTransfer(false, this);
+ cap.setText(contents.toString());
+ Frame frame = new Frame();
+ frame.add(cap);
+ jalview.bin.JalviewLite.addFrame(frame, "Alignment Properties: "
+ + getTitle(), 400, 250);
+ }
+ 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 == sortLengthMenuItem)
+ {
+ sortLengthMenuItem_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);
+ }
+
+ 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(),
+ ((Alignment) viewport.alignment).alignmentProperties);
+
+ if (displayTextbox)
+ {
+ 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;
+ }
+
+ private Hashtable getDisplayedFeatureCols()
+ {
+ if (alignPanel.getFeatureRenderer() != null)
+ {
+ FeatureRenderer fr = alignPanel.getFeatureRenderer();
+ Hashtable fcols = new Hashtable();
+ Enumeration en = viewport.featuresDisplayed.keys();
+ while (en.hasMoreElements())
+ {
+ Object col = en.nextElement();
+ fcols.put(col, fr.featureColours.get(col));
+ }
+ return fcols;
+ }
+ return null;
+ }
+
+ public String outputFeatures(boolean displayTextbox, String format)
+ {
+ String features;
+ if (format.equalsIgnoreCase("Jalview"))
+ {
+ features = new FeaturesFile().printJalviewFormat(
+ viewport.alignment.getSequencesArray(),
+ getDisplayedFeatureCols());
+ }
+ else
+ {
+ features = new FeaturesFile().printGFFFormat(
+ viewport.alignment.getSequencesArray(),
+ getDisplayedFeatureCols());
+ }
+
+ 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;
+ }
+
+ void launchFullApplication()
+ {
+ StringBuffer url = new StringBuffer(jalviewServletURL);
+
+ url.append("?open="
+ + appendProtocol(viewport.applet.getParameter("file")));
+
+ if (viewport.applet.getParameter("features") != null)
+ {
+ url.append("&features=");
+ url.append(appendProtocol(viewport.applet.getParameter("features")));
+ }
+
+ if (viewport.applet.getParameter("annotations") != null)
+ {
+ url.append("&annotations=");
+ url.append(appendProtocol(viewport.applet.getParameter("annotations")));
+ }
+
+ if (viewport.applet.getParameter("jnetfile") != null)
+ {
+ url.append("&annotations=");
+ url.append(appendProtocol(viewport.applet.getParameter("jnetfile")));
+ }
+
+ if (viewport.applet.getParameter("defaultColour") != null)
+ {
+ url.append("&colour="
+ + removeWhiteSpace(viewport.applet
+ .getParameter("defaultColour")));
+ }
+
+ if (viewport.applet.getParameter("userDefinedColour") != null)
+ {
+ url.append("&colour="
+ + removeWhiteSpace(viewport.applet
+ .getParameter("userDefinedColour")));
+ }
+ if (viewport.applet.getParameter("tree") != null)
+ {
+ url.append("&tree="
+ + appendProtocol(viewport.applet.getParameter("tree")));
+ }
+ if (viewport.applet.getParameter("treeFile") != null)
+ {
+ url.append("&tree="
+ + appendProtocol(viewport.applet.getParameter("treeFile")));
+ }
+
+ 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);
+ url = URLEncoder.encode(url);
+ }
+ /*
+ * When we finally deprecate 1.1 compatibility, we can start to use
+ * URLEncoder.encode(url,"UTF-8") and then we'll need this catch: catch
+ * (UnsupportedEncodingException ex) { System.err.println("WARNING -
+ * IMPLEMENTATION ERROR - UNSUPPORTED ENCODING EXCEPTION FOR "+url);
+ * ex.printStackTrace(); }
+ */
+ catch (java.net.MalformedURLException ex)
+ {
+ url = viewport.applet.getCodeBase() + url;
+ }
+ return url;
+ }
+
+ public void closeMenuItem_actionPerformed()
+ {
+ PaintRefresher.RemoveComponent(alignPanel);
+ PaintRefresher.RemoveComponent(alignPanel.seqPanel.seqCanvas);
+ PaintRefresher.RemoveComponent(alignPanel.idPanel.idCanvas);
+
+ if (PaintRefresher.components.size() == 0 && viewport.applet == null)
+ {
+ System.exit(0);
+ }
+
+ this.dispose();
+ }
+
+ /**
+ * DOCUMENT ME!
+ */
+ void updateEditMenuBar()
+ {
+
+ if (viewport.historyList.size() > 0)
+ {
+ undoMenuItem.setEnabled(true);
+ CommandI command = (CommandI) viewport.historyList.peek();
+ undoMenuItem.setLabel("Undo " + command.getDescription());
+ }
+ else
+ {
+ undoMenuItem.setEnabled(false);
+ undoMenuItem.setLabel("Undo");
+ }
+
+ if (viewport.redoList.size() > 0)
+ {
+ redoMenuItem.setEnabled(true);
+
+ CommandI command = (CommandI) viewport.redoList.peek();
+ redoMenuItem.setLabel("Redo " + command.getDescription());
+ }
+ else
+ {
+ redoMenuItem.setEnabled(false);
+ redoMenuItem.setLabel("Redo");
+ }
+ }
+
+ public void addHistoryItem(CommandI command)
+ {
+ if (command.getSize() > 0)
+ {
+ viewport.historyList.push(command);
+ viewport.redoList.removeAllElements();
+ updateEditMenuBar();
+ viewport.hasHiddenColumns = viewport.colSel.getHiddenColumns() != null;
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
+ */
+ protected void undoMenuItem_actionPerformed()
+ {
+ if (viewport.historyList.size() < 1)
+ {
+ return;
+ }
+
+ CommandI command = (CommandI) viewport.historyList.pop();
+ viewport.redoList.push(command);
+ command.undoCommand(null);
+
+ AlignViewport originalSource = getOriginatingSource(command);
+
+ originalSource.hasHiddenColumns = viewport.colSel.getHiddenColumns() != null;
+ updateEditMenuBar();
+ originalSource.firePropertyChange("alignment", null,
+ originalSource.alignment.getSequences());
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
+ */
+ protected void redoMenuItem_actionPerformed()
+ {
+ if (viewport.redoList.size() < 1)
+ {
+ return;
+ }
+
+ CommandI command = (CommandI) viewport.redoList.pop();
+ viewport.historyList.push(command);
+ command.doCommand(null);
+
+ 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)
+ {
+ EditCommand editCommand = (EditCommand) command;
+ al = editCommand.getAlignment();
+ Vector comps = (Vector) PaintRefresher.components.get(viewport
+ .getSequenceSetId());
+ for (int i = 0; i < comps.size(); i++)
+ {
+ if (comps.elementAt(i) instanceof AlignmentPanel)
+ {
+ if (al == ((AlignmentPanel) comps.elementAt(i)).av.alignment)
+ {
+ originalSource = ((AlignmentPanel) comps.elementAt(i)).av;
+ break;
+ }
+ }
+ }
+ }
+
+ if (originalSource == null)
+ {
+ // The original view is closed, we must validate
+ // the current view against the closed view first
+ if (al != null)
+ {
+ PaintRefresher.validateSequences(al, viewport.alignment);
+ }
+
+ originalSource = viewport;
+ }
+
+ return originalSource;
+ }
+
+ public void moveSelectedSequences(boolean up)
+ {
+ SequenceGroup sg = viewport.getSelectionGroup();
+ if (sg == null)
+ {
+ return;
+ }
+
+ if (up)
+ {
+ for (int i = 1; i < viewport.alignment.getHeight(); i++)
+ {
+ SequenceI seq = viewport.alignment.getSequenceAt(i);
+ if (!sg.getSequences(null).contains(seq))
+ {
+ continue;
+ }
+
+ SequenceI temp = viewport.alignment.getSequenceAt(i - 1);
+ if (sg.getSequences(null).contains(temp))
+ {
+ continue;
+ }
+
+ viewport.alignment.getSequences().setElementAt(temp, i);
+ viewport.alignment.getSequences().setElementAt(seq, i - 1);
+ }
+ }
+ else
+ {
+ for (int i = viewport.alignment.getHeight() - 2; i > -1; i--)
+ {
+ SequenceI seq = viewport.alignment.getSequenceAt(i);
+ if (!sg.getSequences(viewport.hiddenRepSequences).contains(seq))
+ {
+ continue;
+ }
+
+ SequenceI temp = viewport.alignment.getSequenceAt(i + 1);
+ if (sg.getSequences(viewport.hiddenRepSequences).contains(temp))
+ {
+ continue;
+ }
+
+ viewport.alignment.getSequences().setElementAt(temp, i);
+ viewport.alignment.getSequences().setElementAt(seq, i + 1);
+ }
+ }
+
+ 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();
+ }
+
+ static StringBuffer copiedSequences;
+
+ static Vector copiedHiddenColumns;
+
+ protected void copy_actionPerformed()
+ {
+ if (viewport.getSelectionGroup() == null)
+ {
+ return;
+ }
+
+ SequenceGroup sg = viewport.getSelectionGroup();
+ copiedSequences = new StringBuffer();
+ Hashtable orderedSeqs = new Hashtable();
+ for (int i = 0; i < sg.getSize(); i++)
+ {
+ SequenceI seq = sg.getSequenceAt(i);
+ int index = viewport.alignment.findIndex(seq);
+ orderedSeqs.put(index + "", seq);
+ }
+
+ 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;
+
+ while (seq == null)
+ {
+ if (orderedSeqs.containsKey(index + ""))
+ {
+ seq = (SequenceI) orderedSeqs.get(index + "");
+ index++;
+
+ break;
+ }
+ else
+ {
+ index++;
+ }
+ }
+
+ // FIND START RES
+ // Returns residue following index if gap
+ startRes = seq.findPosition(sg.getStartRes());
+
+ // FIND END RES
+ // Need to find the residue preceeding index if gap
+ endRes = 0;
+
+ for (int j = 0; j < sg.getEndRes() + 1 && j < seq.getLength(); j++)
+ {
+ ch = seq.getCharAt(j);
+ if (!jalview.util.Comparison.isGap((ch)))
+ {
+ endRes++;
+ }
+ }
+
+ if (endRes > 0)
+ {
+ endRes += seq.getStart() - 1;
+ }
+
+ copiedSequences.append(seq.getName()
+ + "\t"
+ + startRes
+ + "\t"
+ + endRes
+ + "\t"
+ + seq.getSequenceAsString(sg.getStartRes(),
+ sg.getEndRes() + 1) + "\n");
+ }
+
+ }
+
+ protected void pasteNew_actionPerformed()
+ {
+ paste(true);
+ }
+
+ protected void pasteThis_actionPerformed()
+ {
+ paste(false);
+ }
+
+ void paste(boolean newAlignment)
+ {
+ try
+ {
+
+ if (copiedSequences == null)
+ {
+ return;
+ }
+
+ StringTokenizer st = new StringTokenizer(copiedSequences.toString());
+ Vector seqs = new Vector();
+ while (st.hasMoreElements())
+ {
+ String name = st.nextToken();
+ int start = Integer.parseInt(st.nextToken());
+ int end = Integer.parseInt(st.nextToken());
+ 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)
+ {
+ String newtitle = new String("Copied sequences");
+ if (getTitle().startsWith("Copied sequences"))
+ {
+ newtitle = getTitle();
+ }
+ else
+ {
+ 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, DEFAULT_WIDTH,
+ DEFAULT_HEIGHT);
+ }
+ else
+ {
+ addSequences(newSeqs);
+ }
+
+ } catch (Exception ex)
+ {
+ } // could be anything being pasted in here
+
+ }
+
+ void addSequences(SequenceI[] seqs)
+ {
+ 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 cut_actionPerformed()
+ {
+ copy_actionPerformed();
+ delete_actionPerformed();
+ }
+
+ protected void delete_actionPerformed()
+ {
+
+ SequenceGroup sg = viewport.getSelectionGroup();
+ if (sg == null)
+ {
+ return;
+ }
+
+ Vector seqs = new Vector();
+ SequenceI seq;
+ for (int i = 0; i < sg.getSize(); i++)
+ {
+ seq = sg.getSequenceAt(i);
+ seqs.addElement(seq);
+ }
+
+ // 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.firePropertyChange("alignment", null, viewport.getAlignment()
+ .getSequences());
+
+ if (viewport.getAlignment().getHeight() < 1)
+ {
+ this.setVisible(false);
+ }
+ }
+
+ protected void makeGrpsFromSelection_actionPerformed()
+ {
+ if (viewport.getSelectionGroup() != null)
+ {
+ SequenceGroup[] gps = jalview.analysis.Grouping.makeGroupsFrom(
+ viewport.getSequenceSelection(),
+ viewport.getAlignmentView(true).getSequenceStrings(
+ viewport.getGapCharacter()),
+ viewport.alignment.getGroups());
+ viewport.alignment.deleteAllGroups();
+ viewport.sequenceColours = null;
+ viewport.setSelectionGroup(null);
+ // set view properties for each group
+ for (int g = 0; g < gps.length; g++)
+ {
+ // gps[g].setShowunconserved(viewport.getShowUnconserved());
+ gps[g].setshowSequenceLogo(viewport.isShowSequenceLogo());
+ viewport.alignment.addGroup(gps[g]);
+ Color col = new Color((int) (Math.random() * 255),
+ (int) (Math.random() * 255), (int) (Math.random() * 255));
+ col = col.brighter();
+ for (Enumeration sq = gps[g].getSequences(null).elements(); sq
+ .hasMoreElements(); viewport.setSequenceColour(
+ (SequenceI) sq.nextElement(), col))
+ ;
+ }
+ PaintRefresher.Refresh(this, viewport.getSequenceSetId());
+ // alignPanel.updateAnnotation();
+ alignPanel.paintAlignment(true);
+ }
+ }
+
+ protected void deleteGroups_actionPerformed()
+ {
+ viewport.alignment.deleteAllGroups();
+ viewport.sequenceColours = null;
+ viewport.setSelectionGroup(null);
+
+ alignPanel.paintAlignment(true);
+ }
+
+ 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);
+ viewport.setSelectionGroup(sg);
+ alignPanel.paintAlignment(true);
+ PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
+ }
+
+ 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.paintAlignment(true);
+ PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
+ }
+
+ public void invertSequenceMenuItem_actionPerformed()
+ {
+ SequenceGroup sg = viewport.getSelectionGroup();
+ for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
+ {
+ sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
+ }
+
+ PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
+ }
+
+ public void invertColSel_actionPerformed()
+ {
+ viewport.invertColumnSelection();
+ alignPanel.paintAlignment(true);
+ PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
+ }
+
+ void trimAlignment(boolean trimLeft)
+ {
+ ColumnSelection colSel = viewport.getColumnSelection();
+ int column;
+
+ if (colSel.size() > 0)
+ {
+ if (trimLeft)
+ {
+ column = colSel.getMin();
+ }
+ else
+ {
+ column = colSel.getMax();
+ }
+
+ SequenceI[] seqs;
+ if (viewport.getSelectionGroup() != null)
+ {
+ seqs = viewport.getSelectionGroup().getSequencesAsArray(
+ viewport.hiddenRepSequences);
+ }
+ else
+ {
+ seqs = viewport.alignment.getSequencesArray();
+ }
+
+ TrimRegionCommand trimRegion;
+ if (trimLeft)
+ {
+ trimRegion = new TrimRegionCommand("Remove Left",
+ TrimRegionCommand.TRIM_LEFT, seqs, column,
+ viewport.alignment, viewport.colSel,
+ viewport.selectionGroup);
+ viewport.setStartRes(0);
+ }
+ else
+ {
+ trimRegion = new TrimRegionCommand("Remove Right",
+ TrimRegionCommand.TRIM_RIGHT, seqs, column,
+ viewport.alignment, viewport.colSel,
+ viewport.selectionGroup);
+ }
+
+ statusBar.setText("Removed " + trimRegion.getSize() + " columns.");
+
+ addHistoryItem(trimRegion);
+
+ Vector groups = viewport.alignment.getGroups();
+
+ for (int i = 0; i < groups.size(); i++)
+ {
+ SequenceGroup sg = (SequenceGroup) groups.elementAt(i);
+
+ if ((trimLeft && !sg.adjustForRemoveLeft(column))
+ || (!trimLeft && !sg.adjustForRemoveRight(column)))
+ {
+ viewport.alignment.deleteGroup(sg);
+ }
+ }
+
+ viewport.firePropertyChange("alignment", null, viewport
+ .getAlignment().getSequences());
+ }
+ }
+
+ public void removeGappedColumnMenuItem_actionPerformed()
+ {
+ int start = 0, end = viewport.alignment.getWidth() - 1;
+
+ 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();
+ }
+
+ RemoveGapColCommand removeGapCols = new RemoveGapColCommand(
+ "Remove Gapped Columns", seqs, start, end, viewport.alignment);
+
+ addHistoryItem(removeGapCols);
+
+ statusBar.setText("Removed " + removeGapCols.getSize()
+ + " empty columns.");
+
+ // This is to maintain viewport position on first residue
+ // of first sequence
+ SequenceI seq = viewport.alignment.getSequenceAt(0);
+ int startRes = seq.findPosition(viewport.startRes);
+ // ShiftList shifts;
+ // viewport.getAlignment().removeGaps(shifts=new ShiftList());
+ // edit.alColumnChanges=shifts.getInverse();
+ // if (viewport.hasHiddenColumns)
+ // viewport.getColumnSelection().compensateForEdits(shifts);
+ viewport.setStartRes(seq.findIndex(startRes) - 1);
+ viewport.firePropertyChange("alignment", null, viewport.getAlignment()
+ .getSequences());
+
+ }
+
+ public void removeAllGapsMenuItem_actionPerformed()
+ {
+ int start = 0, end = viewport.alignment.getWidth() - 1;
+
+ 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();
+ }
+
+ // 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));
+
+ viewport.setStartRes(seq.findIndex(startRes) - 1);
+
+ viewport.firePropertyChange("alignment", null, viewport.getAlignment()
+ .getSequences());
+
+ }
+
+ public void findMenuItem_actionPerformed()
+ {
+ new Finder(alignPanel);
+ }
+
+ /**
+ * create a new view derived from the current view
+ *
+ * @param viewtitle
+ * @return frame for the new view
+ */
+ public AlignFrame newView(String viewtitle)
+ {
+ AlignmentI newal;
+ if (viewport.hasHiddenRows)
+ {
+ newal = new Alignment(viewport.getAlignment().getHiddenSequences()
+ .getFullAlignment().getSequencesArray());
+ }
+ else
+ {
+ newal = new Alignment(viewport.alignment.getSequencesArray());
+ }
+
+ if (viewport.alignment.getAlignmentAnnotation() != null)
+ {
+ for (int i = 0; i < viewport.alignment.getAlignmentAnnotation().length; i++)
+ {
+ if (!viewport.alignment.getAlignmentAnnotation()[i].autoCalculated)
+ {
+ newal.addAnnotation(viewport.alignment.getAlignmentAnnotation()[i]);
+ }
+ }
+ }
+
+ AlignFrame newaf = new AlignFrame(newal, viewport.applet, "", false);
+
+ newaf.viewport.sequenceSetID = alignPanel.av.getSequenceSetId();
+ PaintRefresher.Register(alignPanel, alignPanel.av.getSequenceSetId());
+ PaintRefresher.Register(newaf.alignPanel,
+ newaf.alignPanel.av.getSequenceSetId());
+
+ PaintRefresher.Register(newaf.alignPanel.idPanel.idCanvas,
+ newaf.alignPanel.av.getSequenceSetId());
+ PaintRefresher.Register(newaf.alignPanel.seqPanel.seqCanvas,
+ newaf.alignPanel.av.getSequenceSetId());
+
+ Vector comps = (Vector) PaintRefresher.components.get(viewport
+ .getSequenceSetId());
+ int viewSize = -1;
+ for (int i = 0; i < comps.size(); i++)
+ {
+ if (comps.elementAt(i) instanceof AlignmentPanel)
+ {
+ viewSize++;
+ }
+ }
+
+ String title = new String(this.getTitle());
+ if (viewtitle != null)
+ {
+ title = viewtitle + " ( " + title + ")";
+ }
+ else
+ {
+ if (title.indexOf("(View") > -1)
+ {
+ title = title.substring(0, title.indexOf("(View"));
+ }
+ title += "(View " + viewSize + ")";
+ }
+
+ newaf.setTitle(title.toString());
+
+ newaf.viewport.historyList = viewport.historyList;
+ newaf.viewport.redoList = viewport.redoList;
+ return newaf;
+ }
+
+ /**
+ *
+ * @return list of feature groups on the view
+ */
+ public String[] getFeatureGroups()
+ {
+ FeatureRenderer fr = null;
+ if (alignPanel != null
+ && (fr = alignPanel.getFeatureRenderer()) != null)
+ {
+ return fr.getGroups();
+ }
+ return null;
+ }
+
+ /**
+ * get sequence feature groups that are hidden or shown
+ *
+ * @param visible
+ * true is visible
+ * @return list
+ */
+ public String[] getFeatureGroupsOfState(boolean visible)
+ {
+ FeatureRenderer fr = null;
+ if (alignPanel != null
+ && (fr = alignPanel.getFeatureRenderer()) != null)
+ {
+ return fr.getGroups(visible);
+ }
+ return null;
+ }
+
+ /**
+ * Change the display state for the given feature groups
+ *
+ * @param groups
+ * list of group strings
+ * @param state
+ * visible or invisible
+ */
+ public void setFeatureGroupState(String[] groups, boolean state)
+ {
+ FeatureRenderer fr = null;
+ this.sequenceFeatures.setState(true);
+ viewport.showSequenceFeatures(true);
+ if (alignPanel != null
+ && (fr = alignPanel.getFeatureRenderer()) != null)
+ {
+ fr.setGroupState(groups, state);
+ alignPanel.seqPanel.seqCanvas.repaint();
+ if (alignPanel.overviewPanel != null)
+ {
+ alignPanel.overviewPanel.updateOverviewImage();
+ }
+ }
+ }
+
+ public void seqLimits_itemStateChanged()
+ {
+ viewport.setShowJVSuffix(seqLimits.getState());
+ alignPanel.fontChanged();
+ alignPanel.paintAlignment(true);
+ }
+
+ protected void colourTextMenuItem_actionPerformed()
+ {
+ viewport.setColourText(colourTextMenuItem.getState());
+ alignPanel.paintAlignment(true);
+ }
+
+ protected void displayNonconservedMenuItem_actionPerformed()
+ {
+ viewport.setShowunconserved(displayNonconservedMenuItem.getState());
+ alignPanel.paintAlignment(true);
+ }
+
+ 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.paintAlignment(true);
+ }
+
+ public void overviewMenuItem_actionPerformed()
+ {
+ if (alignPanel.overviewPanel != null)
+ {
+ return;
+ }
+
+ Frame frame = new Frame();
+ OverviewPanel overview = new OverviewPanel(alignPanel);
+ frame.add(overview);
+ // +50 must allow for applet frame window
+ jalview.bin.JalviewLite.addFrame(frame, "Overview " + this.getTitle(),
+ overview.getPreferredSize().width,
+ overview.getPreferredSize().height + 50);
+
+ frame.pack();
+ frame.addWindowListener(new WindowAdapter()
+ {
+ public void windowClosing(WindowEvent e)
+ {
+ alignPanel.setOverviewPanel(null);
+ };
+ });
+
+ alignPanel.setOverviewPanel(overview);
+
+ }
+
+ void changeColour(ColourSchemeI cs)
+ {
+ int threshold = 0;
+
+ if (cs != null)
+ {
+ if (viewport.getAbovePIDThreshold())
+ {
+ threshold = SliderPanel.setPIDSliderSource(alignPanel, cs,
+ "Background");
+
+ cs.setThreshold(threshold, viewport.getIgnoreGapsConsensus());
+
+ viewport.setGlobalColourScheme(cs);
+ }
+ else
+ {
+ cs.setThreshold(0, viewport.getIgnoreGapsConsensus());
+ }
+
+ if (viewport.getConservationSelected())
+ {
+
+ Alignment al = (Alignment) viewport.alignment;
+ Conservation c = new Conservation("All",
+ ResidueProperties.propHash, 3, al.getSequences(), 0,
+ al.getWidth() - 1);
+
+ c.calculate();
+ c.verdict(false, viewport.ConsPercGaps);
+
+ cs.setConservation(c);
+
+ cs.setConservationInc(SliderPanel.setConservationSlider(alignPanel,
+ cs, "Background"));
+
+ }
+ else
+ {
+ cs.setConservation(null);
+ }
+
+ cs.setConsensus(viewport.hconsensus);
+
+ }
+ viewport.setGlobalColourScheme(cs);
+
+ if (viewport.getColourAppliesToAllGroups())
+ {
+ Vector groups = viewport.alignment.getGroups();
+ for (int i = 0; i < groups.size(); i++)
+ {
+ SequenceGroup sg = (SequenceGroup) groups.elementAt(i);
+
+ if (cs == null)
+ {
+ sg.cs = null;
+ continue;
+ }
+ if (cs instanceof ClustalxColourScheme)
+ {
+ sg.cs = new ClustalxColourScheme(
+ sg.getSequences(viewport.hiddenRepSequences),
+ sg.getWidth());
+ }
+ else
+ {
+ try
+ {
+ sg.cs = (ColourSchemeI) cs.getClass().newInstance();
+ } catch (Exception ex)
+ {
+ ex.printStackTrace();
+ sg.cs = cs;
+ }
+ }
+
+ if (viewport.getAbovePIDThreshold()
+ || cs instanceof PIDColourScheme
+ || cs instanceof Blosum62ColourScheme)
+ {
+ sg.cs.setThreshold(threshold, viewport.getIgnoreGapsConsensus());
+ 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.getSequences(viewport.hiddenRepSequences), 0,
+ viewport.alignment.getWidth() - 1);
+ c.calculate();
+ c.verdict(false, viewport.ConsPercGaps);
+ sg.cs.setConservation(c);
+ }
+ else
+ {
+ sg.cs.setConservation(null);
+ sg.cs.setThreshold(0, viewport.getIgnoreGapsConsensus());
+ }
+
+ }
+ }
+
+ if (alignPanel.getOverviewPanel() != null)
+ {
+ alignPanel.getOverviewPanel().updateOverviewImage();
+ }
+
+ jalview.structure.StructureSelectionManager
+ .getStructureSelectionManager().sequenceColoursChanged(
+ alignPanel);
+
+ alignPanel.paintAlignment(true);
+ }
+
+ protected void modifyPID_actionPerformed()
+ {
+ if (viewport.getAbovePIDThreshold()
+ && viewport.globalColourScheme != null)
+ {
+ SliderPanel.setPIDSliderSource(alignPanel,
+ viewport.getGlobalColourScheme(), "Background");
+ SliderPanel.showPIDSlider();
+ }
+ }
+
+ protected void modifyConservation_actionPerformed()
+ {
+ if (viewport.getConservationSelected()
+ && viewport.globalColourScheme != null)
+ {
+ SliderPanel.setConservationSlider(alignPanel,
+ viewport.globalColourScheme, "Background");
+ SliderPanel.showConservationSlider();
+ }
+ }
+
+ protected void conservationMenuItem_actionPerformed()
+ {
+ viewport.setConservationSelected(conservationMenuItem.getState());
+
+ viewport.setAbovePIDThreshold(false);
+ abovePIDThreshold.setState(false);
+
+ changeColour(viewport.getGlobalColourScheme());
+
+ modifyConservation_actionPerformed();
+ }
+
+ public void abovePIDThreshold_actionPerformed()
+ {
+ viewport.setAbovePIDThreshold(abovePIDThreshold.getState());
+
+ conservationMenuItem.setState(false);
+ viewport.setConservationSelected(false);
+
+ changeColour(viewport.getGlobalColourScheme());
+
+ modifyPID_actionPerformed();
+ }
+
+ public void sortPairwiseMenuItem_actionPerformed()
+ {
+ SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
+ AlignmentSorter.sortByPID(viewport.getAlignment(), viewport
+ .getAlignment().getSequenceAt(0), null);
+
+ addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder,
+ viewport.alignment));
+ alignPanel.paintAlignment(true);
+ }
+
+ public void sortIDMenuItem_actionPerformed()
+ {
+ SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
+ AlignmentSorter.sortByID(viewport.getAlignment());
+ addHistoryItem(new OrderCommand("ID Sort", oldOrder, viewport.alignment));
+ alignPanel.paintAlignment(true);
+ }
+
+ public void sortLengthMenuItem_actionPerformed()
+ {
+ SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
+ AlignmentSorter.sortByLength(viewport.getAlignment());
+ addHistoryItem(new OrderCommand("Length Sort", oldOrder,
+ viewport.alignment));
+ alignPanel.paintAlignment(true);
+ }
+
+ public void sortGroupMenuItem_actionPerformed()
+ {
+ SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
+ AlignmentSorter.sortByGroup(viewport.getAlignment());
+ addHistoryItem(new OrderCommand("Group Sort", oldOrder,
+ viewport.alignment));
+ alignPanel.paintAlignment(true);
+
+ }
+
+ public void removeRedundancyMenuItem_actionPerformed()
+ {
+ new RedundancyPanel(alignPanel);
+ }
+
+ public void pairwiseAlignmentMenuItem_actionPerformed()
+ {
+ if (viewport.getSelectionGroup() != null
+ && viewport.getSelectionGroup().getSize() > 1)
+ {
+ Frame frame = new Frame();
+ frame.add(new PairwiseAlignPanel(alignPanel));
+ jalview.bin.JalviewLite.addFrame(frame, "Pairwise Alignment", 600,
+ 500);
+ }
+ }
+
+ public void PCAMenuItem_actionPerformed()
+ {
+ // are the sequences aligned?
+ if (!viewport.alignment.isAligned(false))
+ {
+ 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 && viewport
+ .getSelectionGroup().getSize() > 0)
+ || viewport.getAlignment().getHeight() < 4)
+ {
+ return;
+ }
+
+ try
+ {
+ new PCAPanel(viewport);
+ } catch (java.lang.OutOfMemoryError ex)
+ {
+ }
+
+ }
+
+ public void averageDistanceTreeMenuItem_actionPerformed()
+ {
+ NewTreePanel("AV", "PID", "Average distance tree using PID");
+ }
+
+ public void neighbourTreeMenuItem_actionPerformed()
+ {
+ NewTreePanel("NJ", "PID", "Neighbour joining tree using PID");
+ }
+
+ protected void njTreeBlosumMenuItem_actionPerformed()
+ {
+ NewTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");
+ }
+
+ protected void avTreeBlosumMenuItem_actionPerformed()
+ {
+ NewTreePanel("AV", "BL", "Average distance tree using BLOSUM62");
+ }
+
+ void NewTreePanel(String type, String pwType, String title)
+ {
+ // are the sequences aligned?
+ if (!viewport.alignment.isAligned(false))
+ {
+ 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() > 1)
+ || (viewport.getSelectionGroup() == null && viewport.alignment
+ .getHeight() > 1))
+ {
+ final TreePanel tp = new TreePanel(viewport, type, pwType);
+
+ addTreeMenuItem(tp, title);
+
+ jalview.bin.JalviewLite.addFrame(tp, title, 600, 500);
+ }
+ }
+
+ 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);
+ }
+
+ 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);
+ }
+
+ /**
+ * sort the alignment using the given treePanel
+ *
+ * @param treePanel
+ * tree used to sort view
+ * @param title
+ * string used for undo event name
+ */
+ public void sortByTree(TreePanel treePanel, String title)
+ {
+ SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
+ AlignmentSorter
+ .sortByTree(viewport.getAlignment(), treePanel.getTree());
+ // addHistoryItem(new HistoryItem("Sort", viewport.alignment,
+ // HistoryItem.SORT));
+ addHistoryItem(new OrderCommand("Order by " + title, oldOrder,
+ viewport.alignment));
+ alignPanel.paintAlignment(true);
+ }
+
+ /**
+ * Do any automatic reordering of the alignment and add the necessary bits to
+ * the menu structure for the new tree
+ *
+ * @param treePanel
+ * @param title
+ */
+ protected void addTreeMenuItem(final TreePanel treePanel,
+ final String title)
+ {
+ final MenuItem item = new MenuItem(title);
+ sortByTreeMenu.add(item);
+ item.addActionListener(new java.awt.event.ActionListener()
+ {
+ public void actionPerformed(ActionEvent evt)
+ {
+ sortByTree(treePanel, title); // treePanel.getTitle());
+ }
+ });
+
+ treePanel.addWindowListener(new WindowAdapter()
+ {
+ public void windowOpened(WindowEvent e)
+ {
+ if (viewport.sortByTree)
+ {
+ sortByTree(treePanel, title);
+ }
+ super.windowOpened(e);
+ }
+
+ public void windowClosing(WindowEvent e)
+ {
+ sortByTreeMenu.remove(item);
+ };
+ });
+ }
+
+ protected void documentation_actionPerformed()
+ {
+ showURL("http://www.jalview.org/help.html", "HELP");
+ }
+
+ protected void about_actionPerformed()
+ {
+
+ class AboutPanel extends Canvas
+ {
+ String version;
+
+ String builddate;
+
+ public AboutPanel(String version, String builddate)
+ {
+ this.version = version;
+ this.builddate = builddate;
+ }
+
+ public void paint(Graphics g)
+ {
+ g.setColor(Color.white);
+ g.fillRect(0, 0, getSize().width, getSize().height);
+ g.setFont(new Font("Helvetica", Font.PLAIN, 12));
+ FontMetrics fm = g.getFontMetrics();
+ int fh = fm.getHeight();
+ int y = 5, x = 7;
+ g.setColor(Color.black);
+ // TODO: update this text for each release or centrally store it for
+ // lite and application
+ g.setFont(new Font("Helvetica", Font.BOLD, 14));
+ g.drawString("JalviewLite - Release " + version, x, y += fh);
+ g.setFont(new Font("Helvetica", Font.BOLD, 12));
+ g.drawString("Build date: " + builddate, x, y += fh);
+ g.setFont(new Font("Helvetica", Font.PLAIN, 12));
+ g.drawString(
+ "Authors: Andrew Waterhouse, Jim Procter, Michele Clamp, James Cuff, Steve Searle,",
+ x, y += fh * 1.5);
+ g.drawString("David Martin & Geoff Barton.", x + 50, y += fh);
+ g.drawString(
+ "Development managed by The Barton Group, University of Dundee, Scotland, UK.",
+ x, y += fh);
+ g.drawString(
+ "For help, see the FAQ at www.jalview.org and/or join the jalview-discuss@jalview.org mailing list",
+ x, y += fh);
+ g.drawString("If you use Jalview, please cite:", x, y += fh + 8);
+ g.drawString(
+ "Waterhouse, A.M., Procter, J.B., Martin, D.M.A, Clamp, M. and Barton, G. J. (2009)",
+ x, y += fh);
+ g.drawString(
+ "Jalview Version 2 - a multiple sequence alignment editor and analysis workbench",
+ x, y += fh);
+ g.drawString("Bioinformatics doi: 10.1093/bioinformatics/btp033",
+ x, y += fh);
+ }
+ }
+
+ Frame frame = new Frame();
+ frame.add(new AboutPanel(JalviewLite.getVersion(), JalviewLite
+ .getBuildDate()));
+ jalview.bin.JalviewLite.addFrame(frame, "Jalview", 580, 220);
+
+ }
+
+ public void showURL(String url, String target)
+ {
+ if (viewport.applet == null)
+ {
+ System.out.println("Not running as applet - no browser available.");
+ }
+ else
+ {
+ try
+ {
+ if (url.indexOf(":") == -1)
+ {
+ // TODO: verify (Bas Vroling bug) prepend codebase or server URL to
+ // form valid URL
+ if (url.indexOf("/") == 0)
+ {
+ String codebase = viewport.applet.getCodeBase().toString();
+ url = codebase.substring(0, codebase.length()
+ - viewport.applet.getCodeBase().getFile().length())
+ + url;
+ }
+ else
+ {
+ url = viewport.applet.getCodeBase() + url;
+ }
+ System.out.println("Show url (prepended codebase): " + url);
+ }
+ else
+ {
+ System.out.println("Show url: " + url);
+ }
+ if (url.indexOf("javascript:") == 0)
+ {
+ // no target for the javascript context
+ viewport.applet.getAppletContext().showDocument(
+ new java.net.URL(url));
+ }
+ else
+ {
+ viewport.applet.getAppletContext().showDocument(
+ new java.net.URL(url), target);
+ }
+ } catch (Exception ex)
+ {
+ ex.printStackTrace();
+ }
+ }
+ }
+
+ // ////////////////////////////////////////////////////////////////////////////////
+ // JBuilder Graphics here
+
+ MenuBar alignFrameMenuBar = new MenuBar();
+
+ Menu fileMenu = new Menu("File");
+
+ MenuItem loadApplication = new MenuItem("View in Full Application");
+
+ MenuItem loadTree = new MenuItem("Load Associated Tree ...");
+
+ MenuItem loadAnnotations = new MenuItem("Load Features/Annotations ...");
+
+ MenuItem outputFeatures = new MenuItem("Export Features ...");
+
+ MenuItem outputAnnotations = new MenuItem("Export Annotations ...");
+
+ MenuItem closeMenuItem = new MenuItem("Close");
+
+ Menu editMenu = new Menu("Edit");
+
+ Menu viewMenu = new Menu("View");
+
+ Menu colourMenu = new Menu("Colour");
+
+ Menu calculateMenu = new Menu("Calculate");
+
+ MenuItem selectAllSequenceMenuItem = new MenuItem("Select all");
+
+ MenuItem deselectAllSequenceMenuItem = new MenuItem("Deselect All");
+
+ MenuItem invertSequenceMenuItem = new MenuItem("Invert Selection");
+
+ MenuItem remove2LeftMenuItem = new MenuItem();
+
+ MenuItem remove2RightMenuItem = new MenuItem();
+
+ MenuItem removeGappedColumnMenuItem = new MenuItem();
+
+ MenuItem removeAllGapsMenuItem = new MenuItem();
+
+ CheckboxMenuItem viewBoxesMenuItem = new CheckboxMenuItem();
+
+ CheckboxMenuItem viewTextMenuItem = new CheckboxMenuItem();
+
+ MenuItem sortPairwiseMenuItem = new MenuItem();
+
+ MenuItem sortIDMenuItem = new MenuItem();
+
+ MenuItem sortLengthMenuItem = new MenuItem();
+
+ MenuItem sortGroupMenuItem = new MenuItem();
+
+ MenuItem removeRedundancyMenuItem = new MenuItem();
+
+ MenuItem pairwiseAlignmentMenuItem = new MenuItem();
+
+ MenuItem PCAMenuItem = new MenuItem();
+
+ MenuItem averageDistanceTreeMenuItem = new MenuItem();
+
+ MenuItem neighbourTreeMenuItem = new MenuItem();
+
+ BorderLayout borderLayout1 = new BorderLayout();
+
+ public Label statusBar = new Label();
+
+ Menu outputTextboxMenu = new Menu();
+
+ MenuItem clustalColour = new MenuItem();
+
+ MenuItem zappoColour = new MenuItem();
+
+ MenuItem taylorColour = new MenuItem();
+
+ MenuItem hydrophobicityColour = new MenuItem();
+
+ MenuItem helixColour = new MenuItem();
+
+ MenuItem strandColour = new MenuItem();
+
+ MenuItem turnColour = new MenuItem();
+
+ MenuItem buriedColour = new MenuItem();
+
+ MenuItem userDefinedColour = new MenuItem();
+
+ MenuItem PIDColour = new MenuItem();
+
+ MenuItem BLOSUM62Colour = new MenuItem();
+
+ MenuItem njTreeBlosumMenuItem = new MenuItem();
+
+ MenuItem avDistanceTreeBlosumMenuItem = new MenuItem();
+
+ CheckboxMenuItem annotationPanelMenuItem = new CheckboxMenuItem();
+
+ CheckboxMenuItem colourTextMenuItem = new CheckboxMenuItem();
+
+ CheckboxMenuItem displayNonconservedMenuItem = new CheckboxMenuItem();
+
+ MenuItem alProperties = new MenuItem("Alignment Properties...");
+
+ MenuItem overviewMenuItem = new MenuItem();
+
+ MenuItem undoMenuItem = new MenuItem();
+
+ MenuItem redoMenuItem = new MenuItem();
+
+ CheckboxMenuItem conservationMenuItem = new CheckboxMenuItem();
+
+ MenuItem noColourmenuItem = new MenuItem();
+
+ CheckboxMenuItem wrapMenuItem = new CheckboxMenuItem();
+
+ CheckboxMenuItem renderGapsMenuItem = new CheckboxMenuItem();
+
+ MenuItem findMenuItem = new MenuItem();
+
+ CheckboxMenuItem abovePIDThreshold = new CheckboxMenuItem();
+
+ MenuItem nucleotideColour = new MenuItem();
+
+ MenuItem deleteGroups = new MenuItem();
+
+ MenuItem grpsFromSelection = 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();
+
+ CheckboxMenuItem applyToAllGroups = new CheckboxMenuItem();
+
+ MenuItem font = new MenuItem();
+
+ CheckboxMenuItem scaleAbove = new CheckboxMenuItem();
+
+ CheckboxMenuItem scaleLeft = new CheckboxMenuItem();
+
+ CheckboxMenuItem scaleRight = new CheckboxMenuItem();
+
+ MenuItem modifyPID = new MenuItem();
+
+ MenuItem modifyConservation = new MenuItem();
+
+ CheckboxMenuItem autoCalculate = new CheckboxMenuItem(
+ "Autocalculate Consensus", true);
+
+ 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();
+
+ CheckboxMenuItem seqLimits = new CheckboxMenuItem();
+
+ CheckboxMenuItem centreColumnLabelFlag = new CheckboxMenuItem();
+
+ CheckboxMenuItem followMouseOverFlag = new CheckboxMenuItem();
+
+ 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);
+ sortLengthMenuItem.setLabel("by Length");
+ sortLengthMenuItem.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);
+ displayNonconservedMenuItem.setLabel("Show nonconserved");
+ displayNonconservedMenuItem.addItemListener(this);
+ alProperties.addActionListener(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);
+ grpsFromSelection.setLabel("Make Groups for selection");
+ grpsFromSelection.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);
+ centreColumnLabelFlag.setLabel("Centre column labels");
+ centreColumnLabelFlag.addItemListener(this);
+ followMouseOverFlag.setLabel("Automatic Scrolling");
+ followMouseOverFlag.addItemListener(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");
+ hideAllButSelection.setLabel("All but Selected Region (Shift+Ctrl+H)");
+ hideAllSelection.setLabel("Selected Region");
+ showAllHidden.setLabel("All Sequences and Columns");
+ invertColSel.addActionListener(this);
+ showColumns.addActionListener(this);
+ showSeqs.addActionListener(this);
+ hideColumns.addActionListener(this);
+ hideSequences.addActionListener(this);
+ hideAllButSelection.addActionListener(this);
+ hideAllSelection.addActionListener(this);
+ showAllHidden.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(followMouseOverFlag);
+ viewMenu.add(annotationPanelMenuItem);
+ viewMenu.addSeparator();
+ viewMenu.add(sequenceFeatures);
+ viewMenu.add(featureSettings);
+ viewMenu.addSeparator();
+ viewMenu.add(alProperties);
+ 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(sortLengthMenuItem);
+ 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);
+ menu1.add(showAllHidden);
+ menu2.add(hideColumns);
+ menu2.add(hideSequences);
+ menu2.add(hideAllSelection);
+ menu2.add(hideAllButSelection);
+ 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(displayNonconservedMenuItem);
+ formatMenu.add(renderGapsMenuItem);
+ formatMenu.add(centreColumnLabelFlag);
+ selectMenu.add(findMenuItem);
+ selectMenu.addSeparator();
+ selectMenu.add(selectAllSequenceMenuItem);
+ selectMenu.add(deselectAllSequenceMenuItem);
+ selectMenu.add(invertSequenceMenuItem);
+ selectMenu.add(invertColSel);
+ selectMenu.add(grpsFromSelection);
+ selectMenu.add(deleteGroups);
+
+ }
+
+ 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();
+
+ MenuItem hideAllButSelection = new MenuItem();
+
+ MenuItem hideAllSelection = new MenuItem();
+
+ MenuItem showAllHidden = new MenuItem();
+
+ Menu formatMenu = new Menu();
+
+ Menu selectMenu = new Menu();
+
+ MenuItem newView = new MenuItem();
+
+ /**
+ * Attach the alignFrame panels after embedding menus, if necessary. This used
+ * to be called setEmbedded, but is now creates the dropdown menus in a
+ * platform independent manner to avoid OSX/Mac menu appendage daftness.
+ *
+ * @param reallyEmbedded
+ * true to attach the view to the applet area on the page rather than
+ * in a new window
+ */
+ public void createAlignFrameWindow(boolean reallyEmbedded, String title)
+ {
+ if (reallyEmbedded)
+ {
+ // ////
+ // Explicly build the embedded menu panel for the on-page applet
+ //
+ // view cannot be closed if its actually on the page
+ fileMenu.remove(closeMenuItem);
+ fileMenu.remove(3); // Remove Seperator
+ embeddedMenu = makeEmbeddedPopupMenu(alignFrameMenuBar, "Arial",
+ Font.PLAIN, 10, false); // use our own fonts.
+ // and actually add the components to the applet area
+ 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();
+ }
+ else
+ {
+ // //////
+ // test and embed menu bar if necessary.
+ //
+ if (embedMenuIfNeeded(alignPanel))
+ {
+ // adjust for status bar height too
+ alignPanel.setSize(getSize().width, getSize().height
+ - statusBar.HEIGHT);
+ }
+ add(statusBar, BorderLayout.SOUTH);
+ add(alignPanel, BorderLayout.CENTER);
+ // and register with the applet so it can pass external API calls to us
+ jalview.bin.JalviewLite.addFrame(this, title, DEFAULT_WIDTH,
+ DEFAULT_HEIGHT);
+ }
+ }
+
+ /**
+ * create a new binding between structures in an existing jmol viewer instance
+ * and an alignpanel with sequences that have existing PDBFile entries. Note,
+ * this does not open a new Jmol window, or modify the display of the
+ * structures in the original jmol window. Note
+ *
+ * @param viewer
+ * JmolViewer instance
+ * @param sequenceIds
+ * - sequence Ids to search for associations
+ * This method doesn't work. See http://issues.jalview.org/browse/JAL-621
+ *
+ public SequenceStructureBinding addStructureViewInstance(Object jmolviewer, String[] sequenceIds)
+ {
+ org.jmol.api.JmolViewer viewer=null;
+ try {
+ viewer = (org.jmol.api.JmolViewer) jmolviewer;
+ }
+ catch (ClassCastException ex) {
+ System.err.println("Unsupported viewer object :"+jmolviewer.getClass());
+ }
+ if (viewer==null)
+ {
+ System.err.println("Can't use this object as a structure viewer:"+jmolviewer.getClass());
+ return null;
+ }
+ SequenceI[] seqs=null;
+ if (sequenceIds==null || sequenceIds.length==0)
+ {
+ seqs = viewport.getAlignment().getSequencesArray();
+ } else {
+ Vector sqi=new Vector();
+ AlignmentI al = viewport.getAlignment();
+ for (int sid=0;sid<sequenceIds.length;sid++) {
+ SequenceI sq = al.findName(sequenceIds[sid]);
+ if (sq!=null) {
+ sqi.addElement(sq);
+ }
+ }
+ if (sqi.size()>0) {
+ seqs = new SequenceI[sqi.size()];
+ for (int sid=0,sSize=sqi.size();sid<sSize;sid++)
+ {
+ seqs[sid] = (SequenceI) sqi.elementAt(sid);
+ }
+ } else {
+ return null;
+ }
+ }
+ ExtJmol jmv=null;
+ // TODO: search for a jmv that involves viewer
+ if (jmv==null){
+ // create a new viewer/jalview binding.
+ jmv = new ExtJmol(viewer, alignPanel, seqs);
+ }
+ return jmv;
+
+ }
+ **/
+ public boolean addPdbFile(String sequenceId, String pdbEntryString,
+ String pdbFile)
+ {
+ SequenceI toaddpdb = viewport.getAlignment().findName(sequenceId);
+ boolean needtoadd = false;
+ if (toaddpdb != null)
+ {
+ Vector pdbe = toaddpdb.getPDBId();
+ PDBEntry pdbentry = null;
+ if (pdbe != null && pdbe.size() > 0)
+ {
+ for (int pe = 0, peSize = pdbe.size(); pe < peSize; pe++)
+ {
+ pdbentry = (PDBEntry) pdbe.elementAt(pe);
+ if (!pdbentry.getId().equals(pdbEntryString)
+ && !pdbentry.getFile().equals(pdbFile))
+ {
+ pdbentry = null;
+ }
+ else
+ {
+ continue;
+ }
+ }
+ }
+ if (pdbentry == null)
+ {
+ pdbentry = new PDBEntry();
+ pdbentry.setId(pdbEntryString);
+ pdbentry.setFile(pdbFile);
+ needtoadd = true; // add this new entry to sequence.
+ }
+ // resolve data source
+ // TODO: this code should be a refactored to an io package
+ String protocol = AppletFormatAdapter.resolveProtocol(pdbFile, "PDB");
+ if (protocol == null)
+ {
+ return false;
+ }
+ if (needtoadd)
+ {
+ // make a note of the access mode and add
+ if (pdbentry.getProperty()==null)
+ {pdbentry.setProperty(new Hashtable());}
+ pdbentry.getProperty().put("protocol", protocol);
+ toaddpdb.addPDBId(pdbentry);
+ }
+ }
+ return true;
+ }
+ private Object[] cleanSeqChainArrays(SequenceI[] seqs, String[] chains)
+ {
+ if (seqs != null)
+ {
+ Vector sequences = new Vector();
+ for (int i = 0; i < seqs.length; i++)
+ {
+ if (seqs[i] != null)
+ {
+ sequences.addElement(new Object[] { seqs[i], (chains!=null) ? chains[i] : null});
+ }
+ }
+ seqs = new SequenceI[sequences.size()];
+ chains = new String[sequences.size()];
+ for (int i = 0, isize = sequences.size(); i < isize; i++)
+ {
+ Object[] oj = (Object[]) sequences.elementAt(i);
+
+ seqs[i] = (SequenceI) oj[0];
+ chains[i] = (String) oj[1];
+ }
+ }
+ return new Object[] { seqs, chains};
+
+ }
+ public void newStructureView(JalviewLite applet, PDBEntry pdb,
+ SequenceI[] seqs, String[] chains, String protocol)
+ {
+ // Scrub any null sequences from the array
+ Object[] sqch = cleanSeqChainArrays(seqs, chains);
+ seqs = (SequenceI[]) sqch[0];
+ chains = (String[]) sqch[1];
+ if (seqs == null || seqs.length == 0)
+ {
+ System.err
+ .println("JalviewLite.AlignFrame:newStructureView: No sequence to bind structure to.");
+ }
+ if (protocol == null || protocol.trim().length() == 0
+ || protocol.equals("null"))
+ {
+ protocol = (String) pdb.getProperty().get("protocol");
+ if (protocol == null)
+ {
+ System.err.println("Couldn't work out protocol to open structure: "
+ + pdb.getId());
+ return;
+ }
+ }
+ if (applet.isAlignPdbStructures() && applet.jmolAvailable)
+ {
+ // can only do alignments with Jmol
+ // find the last jmol window assigned to this alignment
+ jalview.appletgui.AppletJmol ajm = null, tajm;
+ Vector jmols = applet
+ .getAppletWindow(jalview.appletgui.AppletJmol.class);
+ for (int i = 0, iSize = jmols.size(); i < iSize; i++)
+ {
+ tajm = (jalview.appletgui.AppletJmol) jmols.elementAt(i);
+ if (tajm.ap.alignFrame == this)
+ {
+ ajm = tajm;
+ break;
+ }
+ }
+ if (ajm!=null)
+ {
+ System.err.println("Incremental adding and aligning structure to existing Jmol view not yet implemented.");
+ // try and add the pdb structure
+ // ajm.addS
+ ajm = null;
+ }
+ }
+ // otherwise, create a new window
+ if (applet.jmolAvailable)
+ {
+ new jalview.appletgui.AppletJmol(pdb, seqs, chains, alignPanel,
+ protocol);
+ applet.lastFrameX += 40;
+ applet.lastFrameY += 40;
+ }
+ else
+ {
+ new MCview.AppletPDBViewer(pdb, seqs, chains, alignPanel, protocol);
+ }
+
+ }
+
+ public void alignedStructureView(JalviewLite applet, PDBEntry[] pdb,
+ SequenceI[][] seqs, String[][] chains, String[] protocols)
+ {
+ // TODO Auto-generated method stub
+ System.err.println("Aligned Structure View: Not yet implemented.");
+ }
+}
git://source.jalview.org / jalview.git / blobdiff