From: amwaterhouse Date: Mon, 21 Aug 2006 14:13:49 +0000 (+0000) Subject: 1.1 compatible X-Git-Tag: Release_2_1~19 X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=279f73359584dd952a06668b034d2ed98818e315;p=jalview.git 1.1 compatible --- diff --git a/src/jalview/appletgui/AlignFrame.java b/src/jalview/appletgui/AlignFrame.java index 0f7ac3e..c4bf8bf 100755 --- a/src/jalview/appletgui/AlignFrame.java +++ b/src/jalview/appletgui/AlignFrame.java @@ -1,2400 +1,2400 @@ -/* - * Jalview - A Sequence Alignment Editor and Viewer - * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle - * - * This program is free software; you can redistribute it and/or - * modify it under the terms of the GNU General Public License - * as published by the Free Software Foundation; either version 2 - * of the License, or (at your option) any later version. - * - * This program 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 this program; if not, write to the Free Software - * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA - */ - -package jalview.appletgui; - -import jalview.schemes.*; -import jalview.datamodel.*; -import jalview.analysis.*; -import jalview.io.*; -import java.awt.*; -import java.awt.event.*; -import java.util.*; -import java.io.InputStreamReader; -import java.io.BufferedReader; -import java.net.URL; - - -public class AlignFrame extends Frame implements ActionListener, - ItemListener, KeyListener, MouseListener -{ - public AlignmentPanel alignPanel; - public AlignViewport viewport; - int NEW_WINDOW_WIDTH = 700; - int NEW_WINDOW_HEIGHT = 500; - - String jalviewServletURL; - - - public AlignFrame(AlignmentI al, - jalview.bin.JalviewLite applet, - String title, - boolean embedded) - { - - jalviewServletURL = applet.getParameter("APPLICATION_URL"); - - try{ - jbInit(); - }catch(Exception ex) - { - ex.printStackTrace(); - } - - viewport = new AlignViewport(al, applet); - alignPanel = new AlignmentPanel(this, viewport); - - annotationPanelMenuItem.setState(viewport.showAnnotation); - - seqLimits.setState(viewport.showJVSuffix); - - if(applet!=null) - { - String param = applet.getParameter("sortBy"); - if (param != null) - { - if (param.equalsIgnoreCase("Id")) - sortIDMenuItem_actionPerformed(); - else if (param.equalsIgnoreCase("Pairwise Identity")) - sortPairwiseMenuItem_actionPerformed(); - } - - param = applet.getParameter("wrap"); - if (param != null) - { - if (param.equalsIgnoreCase("true")) - { - wrapMenuItem.setState(true); - wrapMenuItem_actionPerformed(); - } - } - - try - { - param = applet.getParameter("windowWidth"); - if (param != null) - { - int width = Integer.parseInt(param); - NEW_WINDOW_WIDTH = width; - } - param = applet.getParameter("windowHeight"); - if (param != null) - { - int height = Integer.parseInt(param); - NEW_WINDOW_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); - - viewport.addPropertyChangeListener(new java.beans.PropertyChangeListener() - { - public void propertyChange(java.beans.PropertyChangeEvent evt) - { - if (evt.getPropertyName().equals("alignment")) - { - alignmentChanged(); - } - } - }); - - - if(embedded) - { - setEmbedded(); - } - else - { - add(alignPanel, BorderLayout.CENTER); - jalview.bin.JalviewLite.addFrame(this, title, NEW_WINDOW_WIDTH, - NEW_WINDOW_HEIGHT); - } - alignPanel.validate(); - alignPanel.repaint(); - } - public AlignViewport getAlignViewport() - { - return viewport; - } - - public SeqCanvas getSeqcanvas() - { - return alignPanel.seqPanel.seqCanvas; - } - - - /** - * DOCUMENT ME! - * - * @param String DOCUMENT ME! - */ - - public void parseFeaturesFile(String file, String type) - { - Hashtable featureLinks = new Hashtable(); - boolean featuresFile = false; - try{ - featuresFile = new jalview.io.FeaturesFile(file, type).parse(viewport.alignment, - alignPanel.seqPanel.seqCanvas. - getFeatureRenderer().featureColours, - featureLinks, - true); - } - catch(Exception ex) - { - ex.printStackTrace(); - } - - if(featuresFile) - { - if(featureLinks.size()>0) - alignPanel.seqPanel.seqCanvas - .getFeatureRenderer().featureLinks = featureLinks; - viewport.showSequenceFeatures = true; - sequenceFeatures.setState(true); - alignPanel.repaint(); - } - - } - - - public void keyPressed(KeyEvent evt) - { - if (viewport.cursorMode - && evt.getKeyCode() >= KeyEvent.VK_0 - && evt.getKeyCode() <= KeyEvent.VK_9) - { - alignPanel.seqPanel.numberPressed(evt.getKeyChar()); - } - - switch (evt.getKeyCode()) - { - case 27: // escape key - deselectAllSequenceMenuItem_actionPerformed(); - break; - case KeyEvent.VK_X: - if (evt.isControlDown() || evt.isMetaDown()) - { - cut_actionPerformed(); - } - break; - case KeyEvent.VK_C: - if (viewport.cursorMode && !evt.isControlDown()) - { - alignPanel.seqPanel.setCursorColumn(); - } - if (evt.isControlDown() || evt.isMetaDown()) - { - copy_actionPerformed(); - } - break; - case KeyEvent.VK_V: - if (evt.isControlDown() || evt.isMetaDown()) - { - paste(true); - } - break; - case KeyEvent.VK_A: - if (evt.isControlDown() || evt.isMetaDown()) - { - selectAllSequenceMenuItem_actionPerformed(); - } - break; - case KeyEvent.VK_DOWN: - if(viewport.cursorMode) - { - alignPanel.seqPanel.moveCursor(0,1); - } - else - moveSelectedSequences(false); - break; - - case KeyEvent.VK_UP: - if (viewport.cursorMode) - { - alignPanel.seqPanel.moveCursor(0,-1); - } - else - moveSelectedSequences(true); - break; - - case KeyEvent.VK_LEFT: - if(viewport.cursorMode) - { - alignPanel.seqPanel.moveCursor(-1,0); - } - break; - - case KeyEvent.VK_RIGHT: - if (viewport.cursorMode) - { - alignPanel.seqPanel.moveCursor(1,0); - } - break; - case KeyEvent.VK_SPACE: - if(viewport.cursorMode) - { - alignPanel.seqPanel.insertGapAtCursor(evt.isControlDown()); - } - break; - - case KeyEvent.VK_DELETE: - case KeyEvent.VK_BACK_SPACE: - if(viewport.cursorMode) - { - alignPanel.seqPanel.deleteGapAtCursor(evt.isControlDown()); - } - else - { - cut_actionPerformed(); - alignPanel.seqPanel.seqCanvas.repaint(); - } - break; - - case KeyEvent.VK_S: - if(viewport.cursorMode) - { - alignPanel.seqPanel.setCursorRow(); - } - break; - case KeyEvent.VK_P: - if(viewport.cursorMode) - { - alignPanel.seqPanel.setCursorPosition(); - } - break; - - case KeyEvent.VK_ENTER: - case KeyEvent.VK_COMMA: - if(viewport.cursorMode) - { - alignPanel.seqPanel.setCursorRowAndColumn(); - } - break; - - case KeyEvent.VK_Q: - if(viewport.cursorMode) - { - alignPanel.seqPanel.setSelectionAreaAtCursor(true); - } - break; - case KeyEvent.VK_M: - if(viewport.cursorMode) - { - alignPanel.seqPanel.setSelectionAreaAtCursor(false); - } - break; - - case KeyEvent.VK_F2: - viewport.cursorMode = ! viewport.cursorMode; - statusBar.setText("Keyboard editing mode is "+ - (viewport.cursorMode ? "on" : "off")); - if(viewport.cursorMode) - { - alignPanel.seqPanel.seqCanvas.cursorX = viewport.startRes; - alignPanel.seqPanel.seqCanvas.cursorY = viewport.startSeq; - } - alignPanel.seqPanel.seqCanvas.repaint(); - break; - - case KeyEvent.VK_F: - if (evt.isControlDown()) - { - findMenuItem_actionPerformed(); - } - break; - case KeyEvent.VK_H: - { - boolean toggleSeqs = !evt.isControlDown(); - boolean toggleCols = !evt.isShiftDown(); - boolean hide = false; - SequenceGroup sg = viewport.getSelectionGroup(); - - if(toggleSeqs) - { - if (sg != null && sg.getSize(false) != 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(); - } - - alignPanel.repaint(); - break; - } - - } - } - public void keyReleased(KeyEvent evt) - {} - public void keyTyped(KeyEvent evt) - {} - -public void itemStateChanged(ItemEvent evt) - { - if(evt.getSource()==colourTextMenuItem) - colourTextMenuItem_actionPerformed(); - else if(evt.getSource()==wrapMenuItem) - wrapMenuItem_actionPerformed(); - else if(evt.getSource()==scaleAbove) - scaleAbove_actionPerformed(); - else if(evt.getSource()==scaleLeft) - scaleLeft_actionPerformed(); - else if(evt.getSource()==scaleRight) - scaleRight_actionPerformed(); - else if(evt.getSource()==seqLimits) - seqLimits_itemStateChanged(); - else if(evt.getSource()==viewBoxesMenuItem) - viewBoxesMenuItem_actionPerformed(); - else if(evt.getSource()==viewTextMenuItem) - viewTextMenuItem_actionPerformed(); - else if(evt.getSource()==renderGapsMenuItem) - renderGapsMenuItem_actionPerformed(); - else if(evt.getSource()==annotationPanelMenuItem) - annotationPanelMenuItem_actionPerformed(); - else if(evt.getSource()==sequenceFeatures) - { - viewport.showSequenceFeatures(sequenceFeatures.getState()); - alignPanel.seqPanel.seqCanvas.repaint(); - } - else if(evt.getSource()==conservationMenuItem) - conservationMenuItem_actionPerformed(); - else if(evt.getSource()==abovePIDThreshold) - abovePIDThreshold_actionPerformed(); - else if(evt.getSource()==applyToAllGroups) - applyToAllGroups_actionPerformed(); - else if(evt.getSource()==autoCalculate) - viewport.autocalculateConsensus = autoCalculate.getState(); - } - public void actionPerformed(ActionEvent evt) - { - Object source = evt.getSource(); - - if(source==inputText) - inputText_actionPerformed(); - else if(source==loadTree) - loadTree_actionPerformed(); - else if(source==loadApplication) - launchFullApplication(); - else if(source==closeMenuItem) - closeMenuItem_actionPerformed(); - else if(source==copy) - copy_actionPerformed(); - else if(source==undoMenuItem) - undoMenuItem_actionPerformed(); - else if(source==redoMenuItem) - redoMenuItem_actionPerformed(); - else if(source==inputText) - inputText_actionPerformed(); - else if(source==closeMenuItem) - closeMenuItem_actionPerformed(); - else if(source==undoMenuItem) - undoMenuItem_actionPerformed(); - else if(source==redoMenuItem) - redoMenuItem_actionPerformed(); - else if(source==copy) - copy_actionPerformed(); - else if(source==pasteNew) - pasteNew_actionPerformed(); - else if(source==pasteThis) - pasteThis_actionPerformed(); - else if(source==cut) - cut_actionPerformed(); - else if(source==delete) - delete_actionPerformed(); - else if(source==deleteGroups) - deleteGroups_actionPerformed(); - else if(source==selectAllSequenceMenuItem) - selectAllSequenceMenuItem_actionPerformed(); - else if(source==deselectAllSequenceMenuItem) - deselectAllSequenceMenuItem_actionPerformed(); - else if(source==invertSequenceMenuItem) - invertSequenceMenuItem_actionPerformed(); - else if(source==invertColSel) - { viewport.invertColumnSelection(); alignPanel.repaint(); } - else if(source==remove2LeftMenuItem) - remove2LeftMenuItem_actionPerformed(); - else if(source==remove2RightMenuItem) - remove2RightMenuItem_actionPerformed(); - else if(source==removeGappedColumnMenuItem) - removeGappedColumnMenuItem_actionPerformed(); - else if(source==removeAllGapsMenuItem) - removeAllGapsMenuItem_actionPerformed(); - else if(source==findMenuItem) - findMenuItem_actionPerformed(); - else if(source==font) - font_actionPerformed(); - else if(source==showColumns) - { - viewport.showAllHiddenColumns(); alignPanel.repaint(); - } - else if(source==showSeqs) - { - viewport.showAllHiddenSeqs(); - } - else if(source == hideColumns) - { - viewport.hideSelectedColumns(); alignPanel.repaint(); - } - else if(source == hideSequences && viewport.getSelectionGroup()!=null) - { - viewport.hideAllSelectedSeqs(); - } - else if(source==featureSettings) - featureSettings_actionPerformed(); - else if(source==overviewMenuItem) - overviewMenuItem_actionPerformed(); - else if(source==noColourmenuItem) - noColourmenuItem_actionPerformed(); - else if(source==clustalColour) - clustalColour_actionPerformed(); - else if(source==zappoColour) - zappoColour_actionPerformed(); - else if(source==taylorColour) - taylorColour_actionPerformed(); - else if(source==hydrophobicityColour) - hydrophobicityColour_actionPerformed(); - else if(source==helixColour) - helixColour_actionPerformed(); - else if(source==strandColour) - strandColour_actionPerformed(); - else if(source==turnColour) - turnColour_actionPerformed(); - else if(source==buriedColour) - buriedColour_actionPerformed(); - else if(source==nucleotideColour) - nucleotideColour_actionPerformed(); - else if(source==modifyPID) - modifyPID_actionPerformed(); - else if(source==modifyConservation) - modifyConservation_actionPerformed(); - else if(source==userDefinedColour) - userDefinedColour_actionPerformed(); - else if(source==PIDColour) - PIDColour_actionPerformed(); - else if(source==BLOSUM62Colour) - BLOSUM62Colour_actionPerformed(); - else if(source==annotationColour) - new AnnotationColourChooser(viewport, alignPanel); - else if(source==sortPairwiseMenuItem) - sortPairwiseMenuItem_actionPerformed(); - else if(source==sortIDMenuItem) - sortIDMenuItem_actionPerformed(); - else if(source==sortGroupMenuItem) - sortGroupMenuItem_actionPerformed(); - else if(source==removeRedundancyMenuItem) - removeRedundancyMenuItem_actionPerformed(); - else if(source==pairwiseAlignmentMenuItem) - pairwiseAlignmentMenuItem_actionPerformed(); - else if(source==PCAMenuItem) - PCAMenuItem_actionPerformed(); - else if(source==averageDistanceTreeMenuItem) - averageDistanceTreeMenuItem_actionPerformed(); - else if(source==neighbourTreeMenuItem) - neighbourTreeMenuItem_actionPerformed(); - else if(source==njTreeBlosumMenuItem) - njTreeBlosumMenuItem_actionPerformed(); - else if(source==avDistanceTreeBlosumMenuItem) - avTreeBlosumMenuItem_actionPerformed(); - else if(source==documentation) - documentation_actionPerformed(); - else if(source==about) - about_actionPerformed(); - - } - - public void inputText_actionPerformed() - { - CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this); - Frame frame = new Frame(); - frame.add(cap); - jalview.bin.JalviewLite.addFrame(frame, "Cut & Paste Input", 500, 500); - } - - protected void outputText_actionPerformed(ActionEvent e) - { - CutAndPasteTransfer cap = new CutAndPasteTransfer(false, this); - Frame frame = new Frame(); - frame.add(cap); - jalview.bin.JalviewLite.addFrame(frame, - "Alignment output - " + e.getActionCommand(), - 600, 500); - cap.setText(new AppletFormatAdapter().formatSequences(e.getActionCommand(), - viewport.getAlignment().getSequences(), - viewport.showJVSuffix)); - } - - void launchFullApplication() - { - StringBuffer url = new StringBuffer(jalviewServletURL); - - url.append("?open="+ - appendProtocol( viewport.applet.getParameter("file") ) ); - - if(viewport.applet.getParameter("features")!=null) - { - url.append( "&features=" ); - url.append( appendProtocol( viewport.applet.getParameter("features") ) ); - } - - if(viewport.applet.getParameter("annotations")!=null) - { - url.append( "&annotations=" ); - url.append( appendProtocol( viewport.applet.getParameter("annotations") ) ); - } - - if(viewport.applet.getParameter("defaultColour")!=null) - { - url.append("&colour=" + - removeWhiteSpace(viewport.applet.getParameter("defaultColour")) - ); - } - - if(viewport.applet.getParameter("userDefinedColour")!=null) - { - url.append( "&colour=" + - removeWhiteSpace( viewport.applet.getParameter("userDefinedColour") ) - ); - } - - showURL(url.toString(), "FULL_APP"); - } - - - String removeWhiteSpace(String colour) - { - StringBuffer sb = new StringBuffer(); - for (int i = 0; i < colour.length(); i++) - { - if (Character.isWhitespace(colour.charAt(i))) - sb.append("%20"); - else - sb.append(colour.charAt(i)); - } - - return sb.toString(); - } - - - String appendProtocol(String url) - { - try{ - new URL(url); - }catch(java.net.MalformedURLException ex) - { - url = viewport.applet.getCodeBase()+url; - } - return url; - } - - public void closeMenuItem_actionPerformed() - { - PaintRefresher.components.remove(viewport.alignment); - if(PaintRefresher.components.size()==0 && viewport.applet==null) - System.exit(0); - - this.dispose(); - } - - Stack historyList = new Stack(); - Stack redoList = new Stack(); - - void updateEditMenuBar() - { - if (historyList.size() > 0) - { - undoMenuItem.setEnabled(true); - HistoryItem hi = (HistoryItem) historyList.peek(); - undoMenuItem.setLabel("Undo " + hi.getDescription()); - } - else - { - undoMenuItem.setEnabled(false); - undoMenuItem.setLabel("Undo"); - } - - if (redoList.size() > 0) - { - redoMenuItem.setEnabled(true); - HistoryItem hi = (HistoryItem) redoList.peek(); - redoMenuItem.setLabel("Redo " + hi.getDescription()); - } - else - { - redoMenuItem.setEnabled(false); - redoMenuItem.setLabel("Redo"); - } - } - - public void addHistoryItem(HistoryItem hi) - { - historyList.push(hi); - redoList.clear(); - updateEditMenuBar(); - } - - protected void undoMenuItem_actionPerformed() - { - HistoryItem nh,hi = (HistoryItem) historyList.pop(); - redoList.push(nh=new HistoryItem(hi.getDescription(), viewport.alignment, - HistoryItem.HIDE)); - if (hi.alColumnChanges!=null) - nh.alColumnChanges=hi.alColumnChanges.getInverse(); - restoreHistoryItem(hi); - viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences()); - } - - protected void redoMenuItem_actionPerformed() - { - HistoryItem nh,hi = (HistoryItem) redoList.pop(); - historyList.push(nh=new HistoryItem(hi.getDescription(), viewport.alignment, - HistoryItem.HIDE)); - if (hi.alColumnChanges!=null) - nh.alColumnChanges=hi.alColumnChanges.getInverse(); - restoreHistoryItem(hi); - updateEditMenuBar(); - viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences()); - } - - // used by undo and redo - void restoreHistoryItem(HistoryItem hi) - { - hi.restore(viewport.getColumnSelection()); - updateEditMenuBar(); - - viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences()); - } - - 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(false).contains(seq)) - { - continue; - } - - SequenceI temp = viewport.alignment.getSequenceAt(i - 1); - if (sg.getSequences(false).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(true).contains(seq)) - { - continue; - } - - SequenceI temp = viewport.alignment.getSequenceAt(i + 1); - if (sg.getSequences(true).contains(temp)) - { - continue; - } - - viewport.alignment.getSequences().setElementAt(temp, i); - viewport.alignment.getSequences().setElementAt(seq, i + 1); - } - } - - alignPanel.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(false); 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(false); 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.getSequence(sg.getStartRes(), - sg.getEndRes() + 1) + "\n"); - } - - } - - protected void pasteNew_actionPerformed() - { - paste(true); - } - - protected void pasteThis_actionPerformed() - { - addHistoryItem(new HistoryItem("Paste Sequences", viewport.alignment, - HistoryItem.PASTE)); - 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()); - Sequence sequence = new Sequence(name, st.nextToken(), start, end); - - if (!newAlignment) - { - viewport.alignment.addSequence(sequence); - } - else - { - seqs.addElement(sequence); - } - } - - if (newAlignment) - { - SequenceI[] newSeqs = new SequenceI[seqs.size()]; - for (int i = 0; i < seqs.size(); i++) - { - newSeqs[i] = (SequenceI) seqs.elementAt(i); - } - - 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, NEW_WINDOW_WIDTH, - NEW_WINDOW_HEIGHT); - } - else - { - viewport.setEndSeq(viewport.alignment.getHeight()); - viewport.alignment.getWidth(); - viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences()); - } - - } - catch (Exception ex) - {} // could be anything being pasted in here - - } - - protected void cut_actionPerformed() - { - copy_actionPerformed(); - delete_actionPerformed(); - } - - protected void delete_actionPerformed() - { - addHistoryItem(new HistoryItem("Delete Sequences", viewport.alignment, - HistoryItem.HIDE)); - if (viewport.getSelectionGroup() == null) - { - return; - } - - - SequenceGroup sg = viewport.getSelectionGroup(); - boolean allSequences = false; - if(sg.getSize(false)==viewport.alignment.getHeight()) - allSequences = true; - - for (int i = 0; i < sg.getSize(false); i++) - { - SequenceI seq = sg.getSequenceAt(i); - int index = viewport.getAlignment().findIndex(seq); - seq.deleteChars(sg.getStartRes(), sg.getEndRes() + 1); - - // If the cut affects all sequences, remove highlighted columns - if (allSequences) - { - viewport.getColumnSelection().removeElements(sg.getStartRes(), - sg.getEndRes() + 1); - } - - - if (seq.getSequence().length() < 1) - { - viewport.getAlignment().deleteSequence(seq); - } - else - { - viewport.getAlignment().getSequences().setElementAt(seq, index); - } - } - - viewport.setSelectionGroup(null); - viewport.alignment.deleteGroup(sg); - viewport.resetSeqLimits(alignPanel.seqPanel.seqCanvas.getSize().height); - if (viewport.getAlignment().getHeight() < 1) - { - try - { - this.setVisible(false); - } - catch (Exception ex) - {} - } - viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences()); - - } - - protected void deleteGroups_actionPerformed() - { - viewport.alignment.deleteAllGroups(); - viewport.setSelectionGroup(null); - - alignPanel.repaint(); - } - - 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.repaint(); - PaintRefresher.Refresh(null, viewport.alignment); - } - - public void deselectAllSequenceMenuItem_actionPerformed() - { - if(viewport.cursorMode) - { - alignPanel.seqPanel.keyboardNo1=null; - alignPanel.seqPanel.keyboardNo2=null; - } - viewport.setSelectionGroup(null); - viewport.getColumnSelection().clear(); - viewport.setSelectionGroup(null); - alignPanel.idPanel.idCanvas.searchResults = null; - alignPanel.seqPanel.seqCanvas.highlightSearchResults(null); - alignPanel.repaint(); - PaintRefresher.Refresh(null, viewport.alignment); - } - - public void invertSequenceMenuItem_actionPerformed() - { - SequenceGroup sg = viewport.getSelectionGroup(); - for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++) - { - sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false); - } - - PaintRefresher.Refresh(null, viewport.alignment); - } - - public void remove2LeftMenuItem_actionPerformed() - { - ColumnSelection colSel = viewport.getColumnSelection(); - if (colSel.size() > 0) - { - HistoryItem edit; - addHistoryItem(edit=new HistoryItem("Remove Left", viewport.alignment, - HistoryItem.HIDE)); - int min = colSel.getMin(); - viewport.getAlignment().trimLeft(min); - colSel.compensateForEdit(0, min); - edit.addShift(0, min); - if (viewport.getSelectionGroup() != null) - { - viewport.getSelectionGroup().adjustForRemoveLeft(min); - } - - Vector groups = viewport.alignment.getGroups(); - for (int i = 0; i < groups.size(); i++) - { - SequenceGroup sg = (SequenceGroup) groups.elementAt(i); - if (!sg.adjustForRemoveLeft(min)) - { - viewport.alignment.deleteGroup(sg); - } - } - viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences()); - } - } - - public void remove2RightMenuItem_actionPerformed() - { - ColumnSelection colSel = viewport.getColumnSelection(); - if (colSel.size() > 0) - { - addHistoryItem(new HistoryItem("Remove Right", viewport.alignment, - HistoryItem.HIDE)); - int max = colSel.getMax(); - viewport.getAlignment().trimRight(max); - - if (viewport.getSelectionGroup() != null) - { - viewport.getSelectionGroup().adjustForRemoveRight(max); - } - - Vector groups = viewport.alignment.getGroups(); - for (int i = 0; i < groups.size(); i++) - { - SequenceGroup sg = (SequenceGroup) groups.elementAt(i); - if (!sg.adjustForRemoveRight(max)) - { - viewport.alignment.deleteGroup(sg); - } - } - viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences()); - } - - } - - public void removeGappedColumnMenuItem_actionPerformed() - { - HistoryItem edit; - addHistoryItem(edit=new HistoryItem("Remove Gapped Columns", - viewport.alignment, - HistoryItem.HIDE)); - - //This is to maintain viewport position on first residue - //of first sequence - SequenceI seq = viewport.alignment.getSequenceAt(0); - int startRes = seq.findPosition(viewport.startRes); - - viewport.getAlignment().removeGaps(); - - viewport.setStartRes(seq.findIndex(startRes)-1); - - viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences()); - } - - public void removeAllGapsMenuItem_actionPerformed() - { - // TODO: hidden regions should not be touched by removeAllGaps - a minimal number of gaps will remain in alignment segments containing uneven length subsequences - // TODO: columnSelection.compensateforedits should be called (and passed to history item) - HistoryItem editgaps; - addHistoryItem(editgaps=new HistoryItem("Remove Gaps", viewport.alignment, - HistoryItem.HIDE)); - - //This is to maintain viewport position on first residue - //of first sequence - SequenceI seq = viewport.alignment.getSequenceAt(0); - int startRes = seq.findPosition(viewport.startRes); - - SequenceI current; - Vector seqs=null; - - int start=0, end = viewport.alignment.getWidth(); - - if (viewport.getSelectionGroup() != null - && viewport.getSelectionGroup().getSequences(false) != null - && viewport.getSelectionGroup().getSize(false)>0) - { - seqs = viewport.getSelectionGroup().getSequences(true); - start = viewport.getSelectionGroup().getStartRes(); - end = viewport.getSelectionGroup().getEndRes()+1; - } - else - seqs = viewport.alignment.getSequences(); - - /* Commented out regions below are partial implementation of todo above. - * divide start,end into visible chunks, and for each: - int diff=end-start+1; - int diffmax=0; - int dr[] = new int[seqs.size()]; - */ - for (int i = 0; i < seqs.size(); i++) - { - current = (SequenceI) seqs.elementAt(i); - //dr[i]= - current.removeGaps(start, end); - /*if (d0) { - // record shift for history. - editgaps.addShift(start, diff); - if (viewport.hasHiddenColumns && diffmax>diff) { - // pad sequence - StringBuffer gaps=new StringBuffer(diffmax); - for (int i=0,j=diffmax-diff; i0) { - String sq = current.getSequence(); - current.setSequence(sq.substring(0, hcend-dr[i])+gaps.substring(0, dr[i]-diff)+sq.substring()); - } - } - } - }*/ - - viewport.setStartRes(seq.findIndex(startRes)-1); - viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences()); - } - - public void alignmentChanged() - { - viewport.alignment.padGaps(); - if(viewport.autocalculateConsensus) - { - viewport.updateConsensus(); - viewport.updateConservation(); - } - - resetAllColourSchemes(); - if(alignPanel.overviewPanel!=null) - alignPanel.overviewPanel.updateOverviewImage(); - - viewport.alignment.adjustSequenceAnnotations(); - alignPanel.repaint(); - } - - void resetAllColourSchemes() - { - ColourSchemeI cs = viewport.globalColourScheme; - if(cs!=null) - { - if (cs instanceof ClustalxColourScheme) - { - ( (ClustalxColourScheme) viewport.getGlobalColourScheme()). - resetClustalX(viewport.alignment.getSequences(), - viewport.alignment.getWidth()); - } - - cs.setConsensus(viewport.vconsensus); - if (cs.conservationApplied()) - { - 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); - } - } - - int s, sSize = viewport.alignment.getGroups().size(); - for(s=0; s 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()) - { - SequenceI current; - int Width = viewport.getAlignment().getWidth(); - - for (int i = 0; i < viewport.getAlignment().getSequences().size(); - i++) - { - current = viewport.getAlignment().getSequenceAt(i); - - if (current.getLength() < Width) - { - current.insertCharAt(Width - 1, viewport.getGapCharacter()); - } - } - alignPanel.repaint(); - } - - if ( (viewport.getSelectionGroup() != null && - viewport.getSelectionGroup().getSize(false) < 4 && - viewport.getSelectionGroup().getSize(false) > 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 BLOSUM62PID"); - } - - void NewTreePanel(String type, String pwType, String title) - { - //are the sequences aligned? - if (!viewport.alignment.isAligned()) - { - SequenceI current; - int Width = viewport.getAlignment().getWidth(); - - for (int i = 0; i < viewport.getAlignment().getSequences().size(); - i++) - { - current = viewport.getAlignment().getSequenceAt(i); - - if (current.getLength() < Width) - { - current.insertCharAt(Width - 1, viewport.getGapCharacter()); - } - } - alignPanel.repaint(); - - } - - if ( (viewport.getSelectionGroup() != null && - viewport.getSelectionGroup().getSize(false) > 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.treeImport = true; - Frame frame = new Frame(); - frame.add(cap); - jalview.bin.JalviewLite.addFrame(frame, "Paste Newick file ", 400, 300); - } - - public void loadTree(jalview.io.NewickFile tree, String treeFile) - { - TreePanel tp = new TreePanel(viewport, - treeFile, - "From File - ", - tree); - jalview.bin.JalviewLite.addFrame(tp, treeFile, 600, 500); - addTreeMenuItem(tp, treeFile); - } - - void addTreeMenuItem(final TreePanel treePanel, String title) - { - final MenuItem item = new MenuItem(title); - sortByTreeMenu.add(item); - item.addActionListener(new java.awt.event.ActionListener() - { - public void actionPerformed(ActionEvent evt) - { - addHistoryItem(new HistoryItem("Sort", viewport.alignment, - HistoryItem.SORT)); - AlignmentSorter.sortByTree(viewport.getAlignment(), treePanel.getTree()); - alignPanel.repaint(); - } - }); - - treePanel.addWindowListener(new WindowAdapter() - { - 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; - public AboutPanel(String version) - { this.version = version; } - - 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); - g.setFont(new Font("Helvetica", Font.BOLD, 14)); - g.drawString("Jalview - Release "+version, 200, y += fh); - g.setFont(new Font("Helvetica", Font.PLAIN, 12)); - g.drawString("Authors: Michele Clamp, James Cuff, Steve Searle, Andrew Waterhouse, Jim Procter & Geoff Barton.", - x, y += fh * 2); - g.drawString("Current development managed by Andrew Waterhouse; Barton Group, University of Dundee.", - x, y += fh); - g.drawString( - "For any issues relating to Jalview, email help@jalview.org", x, - y += fh); - g.drawString("If you use JalView, please cite:", x, y += fh + 8); - g.drawString("\"Clamp, M., Cuff, J., Searle, S. M. and Barton, G. J. (2004), The Jalview Java Alignment Editor\"", - x, y += fh); - g.drawString("Bioinformatics, 2004 20;426-7.", x, y += fh); - } - } - - String version = "test"; - java.net.URL url = getClass().getResource("/.build_properties"); - if (url != null) - { - try - { - BufferedReader reader = new BufferedReader(new InputStreamReader( - url.openStream())); - String line; - while ( (line = reader.readLine()) != null) - { - if (line.indexOf("VERSION") > -1) - { - version = line.substring(line.indexOf("=") + 1); - } - } - } - catch (Exception ex) - { - ex.printStackTrace(); - } - } - - - Frame frame = new Frame(); - frame.add(new AboutPanel(version)); - jalview.bin.JalviewLite.addFrame(frame, "Jalview", 580, 200); - - } - - public void showURL(String url, String target) - { - if (viewport.applet == null) - { - System.out.println("Not running as applet - no browser available."); - } - else - { - try - { - System.out.println("Show url: "+url); - viewport.applet.getAppletContext().showDocument(new java.net.URL(url), - target); - } - catch (Exception ex) - { - ex.printStackTrace(); - } - } - } - - - ////////////////////////////////////////////////////////////////////////////////// - //JBuilder Graphics here - - protected MenuBar alignFrameMenuBar = new MenuBar(); - protected Menu fileMenu = new Menu("File"); - protected MenuItem loadApplication = new MenuItem("View in Full Application"); - protected MenuItem loadTree = new MenuItem("Load Associated Tree"); - protected MenuItem closeMenuItem = new MenuItem("Close"); - protected Menu editMenu = new Menu("Edit"); - protected Menu viewMenu = new Menu("View"); - protected Menu colourMenu = new Menu("Colour"); - protected Menu calculateMenu = new Menu("Calculate"); - protected MenuItem selectAllSequenceMenuItem = new MenuItem("Select all"); - protected MenuItem deselectAllSequenceMenuItem = new MenuItem("Deselect All"); - protected MenuItem invertSequenceMenuItem = new MenuItem("Invert Selection"); - protected MenuItem remove2LeftMenuItem = new MenuItem(); - protected MenuItem remove2RightMenuItem = new MenuItem(); - protected MenuItem removeGappedColumnMenuItem = new MenuItem(); - protected MenuItem removeAllGapsMenuItem = new MenuItem(); - protected CheckboxMenuItem viewBoxesMenuItem = new CheckboxMenuItem(); - protected CheckboxMenuItem viewTextMenuItem = new CheckboxMenuItem(); - protected MenuItem sortPairwiseMenuItem = new MenuItem(); - protected MenuItem sortIDMenuItem = new MenuItem(); - protected MenuItem sortGroupMenuItem = new MenuItem(); - protected MenuItem removeRedundancyMenuItem = new MenuItem(); - protected MenuItem pairwiseAlignmentMenuItem = new MenuItem(); - protected MenuItem PCAMenuItem = new MenuItem(); - protected MenuItem averageDistanceTreeMenuItem = new MenuItem(); - protected MenuItem neighbourTreeMenuItem = new MenuItem(); - BorderLayout borderLayout1 = new BorderLayout(); - public Label statusBar = new Label(); - protected Menu outputTextboxMenu = new Menu(); - protected MenuItem clustalColour = new MenuItem(); - protected MenuItem zappoColour = new MenuItem(); - protected MenuItem taylorColour = new MenuItem(); - protected MenuItem hydrophobicityColour = new MenuItem(); - protected MenuItem helixColour = new MenuItem(); - protected MenuItem strandColour = new MenuItem(); - protected MenuItem turnColour = new MenuItem(); - protected MenuItem buriedColour = new MenuItem(); - protected MenuItem userDefinedColour = new MenuItem(); - protected MenuItem PIDColour = new MenuItem(); - protected MenuItem BLOSUM62Colour = new MenuItem(); - MenuItem njTreeBlosumMenuItem = new MenuItem(); - MenuItem avDistanceTreeBlosumMenuItem = new MenuItem(); - protected CheckboxMenuItem annotationPanelMenuItem = new CheckboxMenuItem(); - protected CheckboxMenuItem colourTextMenuItem = new CheckboxMenuItem(); - MenuItem overviewMenuItem = new MenuItem(); - protected MenuItem undoMenuItem = new MenuItem(); - protected MenuItem redoMenuItem = new MenuItem(); - protected CheckboxMenuItem conservationMenuItem = new CheckboxMenuItem(); - MenuItem noColourmenuItem = new MenuItem(); - protected CheckboxMenuItem wrapMenuItem = new CheckboxMenuItem(); - protected CheckboxMenuItem renderGapsMenuItem = new CheckboxMenuItem(); - MenuItem findMenuItem = new MenuItem(); - Menu searchMenu = new Menu(); - protected CheckboxMenuItem abovePIDThreshold = new CheckboxMenuItem(); - protected MenuItem nucleotideColour = new MenuItem(); - MenuItem deleteGroups = new MenuItem(); - MenuItem delete = new MenuItem(); - MenuItem copy = new MenuItem(); - MenuItem cut = new MenuItem(); - Menu pasteMenu = new Menu(); - MenuItem pasteNew = new MenuItem(); - MenuItem pasteThis = new MenuItem(); - protected CheckboxMenuItem applyToAllGroups = new CheckboxMenuItem(); - protected MenuItem font = new MenuItem(); - protected CheckboxMenuItem scaleAbove = new CheckboxMenuItem(); - protected CheckboxMenuItem scaleLeft = new CheckboxMenuItem(); - protected CheckboxMenuItem scaleRight = new CheckboxMenuItem(); - MenuItem modifyPID = new MenuItem(); - MenuItem modifyConservation = new MenuItem(); - protected CheckboxMenuItem autoCalculate - = new CheckboxMenuItem("Autocalculate Consensus", true); - protected Menu sortByTreeMenu = new Menu(); - Menu sort = new Menu(); - Menu calculate = new Menu(); - MenuItem inputText = new MenuItem(); - Menu helpMenu = new Menu(); - MenuItem documentation = new MenuItem(); - MenuItem about = new MenuItem(); - protected CheckboxMenuItem seqLimits = new CheckboxMenuItem(); - Panel embeddedMenu; - Label embeddedEdit; - Label embeddedSearch; - Label embeddedView; - Label embeddedColour; - Label embeddedFile; - Label embeddedHelp; - Label embeddedCalculate; - FlowLayout flowLayout1; - - private void jbInit() throws Exception { - - setMenuBar(alignFrameMenuBar); - - MenuItem item; - - // dynamically fill save as menu with available formats - for (int i = 0; i < jalview.io.AppletFormatAdapter.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); - selectAllSequenceMenuItem.addActionListener(this); - deselectAllSequenceMenuItem.addActionListener(this); - invertSequenceMenuItem.addActionListener(this); - remove2LeftMenuItem.setLabel("Remove Left"); - remove2LeftMenuItem.addActionListener(this); - remove2RightMenuItem.setLabel("Remove Right"); - remove2RightMenuItem.addActionListener(this); - removeGappedColumnMenuItem.setLabel("Remove Empty Columns"); - removeGappedColumnMenuItem.addActionListener(this); - removeAllGapsMenuItem.setLabel("Remove All Gaps"); - removeAllGapsMenuItem.addActionListener(this); - viewBoxesMenuItem.setLabel("Boxes"); - viewBoxesMenuItem.setState(true); - viewBoxesMenuItem.addItemListener(this); - viewTextMenuItem.setLabel("Text"); - viewTextMenuItem.setState(true); - viewTextMenuItem.addItemListener(this); - sortPairwiseMenuItem.setLabel("by Pairwise Identity"); - sortPairwiseMenuItem.addActionListener(this); - sortIDMenuItem.setLabel("by ID"); - sortIDMenuItem.addActionListener(this); - sortGroupMenuItem.setLabel("by Group"); - sortGroupMenuItem.addActionListener(this); - removeRedundancyMenuItem.setLabel("Remove Redundancy..."); - removeRedundancyMenuItem.addActionListener(this); - pairwiseAlignmentMenuItem.setLabel("Pairwise Alignments..."); - pairwiseAlignmentMenuItem.addActionListener(this); - PCAMenuItem.setLabel("Principal Component Analysis"); - PCAMenuItem.addActionListener(this); - averageDistanceTreeMenuItem.setLabel( - "Average Distance Using % Identity"); - averageDistanceTreeMenuItem.addActionListener(this); - neighbourTreeMenuItem.setLabel("Neighbour Joining Using % Identity"); - neighbourTreeMenuItem.addActionListener(this); - alignFrameMenuBar.setFont(new java.awt.Font("Verdana", 0, 11)); - statusBar.setBackground(Color.white); - statusBar.setFont(new java.awt.Font("Verdana", 0, 11)); - statusBar.setText("Status bar"); - outputTextboxMenu.setLabel("Output to Textbox"); - clustalColour.setLabel("Clustalx"); - - clustalColour.addActionListener(this); - zappoColour.setLabel("Zappo"); - zappoColour.addActionListener(this); - taylorColour.setLabel("Taylor"); - taylorColour.addActionListener(this); - hydrophobicityColour.setLabel("Hydrophobicity"); - hydrophobicityColour.addActionListener(this); - helixColour.setLabel("Helix Propensity"); - helixColour.addActionListener(this); - strandColour.setLabel("Strand Propensity"); - strandColour.addActionListener(this); - turnColour.setLabel("Turn Propensity"); - turnColour.addActionListener(this); - buriedColour.setLabel("Buried Index"); - buriedColour.addActionListener(this); - userDefinedColour.setLabel("User Defined..."); - userDefinedColour.addActionListener(this); - PIDColour.setLabel("Percentage Identity"); - PIDColour.addActionListener(this); - BLOSUM62Colour.setLabel("BLOSUM62 Score"); - BLOSUM62Colour.addActionListener(this); - avDistanceTreeBlosumMenuItem.setLabel( - "Average Distance Using BLOSUM62"); - avDistanceTreeBlosumMenuItem.addActionListener(this); - njTreeBlosumMenuItem.setLabel("Neighbour Joining Using BLOSUM62"); - njTreeBlosumMenuItem.addActionListener(this); - annotationPanelMenuItem.setLabel("Show Annotations"); - annotationPanelMenuItem.addItemListener(this); - colourTextMenuItem.setLabel("Colour Text"); - colourTextMenuItem.addItemListener(this); - overviewMenuItem.setLabel("Overview Window"); - overviewMenuItem.addActionListener(this); - undoMenuItem.setEnabled(false); - undoMenuItem.setLabel("Undo"); - undoMenuItem.addActionListener(this); - redoMenuItem.setEnabled(false); - redoMenuItem.setLabel("Redo"); - redoMenuItem.addActionListener(this); - conservationMenuItem.setLabel("by Conservation"); - conservationMenuItem.addItemListener(this); - noColourmenuItem.setLabel("None"); - noColourmenuItem.addActionListener(this); - wrapMenuItem.setLabel("Wrap"); - wrapMenuItem.addItemListener(this); - renderGapsMenuItem.setLabel("Show Gaps"); - renderGapsMenuItem.setState(true); - renderGapsMenuItem.addItemListener(this); - findMenuItem.setLabel("Find..."); - findMenuItem.addActionListener(this); - searchMenu.setLabel("Search"); - - abovePIDThreshold.setLabel("Above Identity Threshold"); - abovePIDThreshold.addItemListener(this); - nucleotideColour.setLabel("Nucleotide"); - nucleotideColour.addActionListener(this); - deleteGroups.setLabel("Undefine Groups"); - deleteGroups.addActionListener(this); - copy.setLabel("Copy"); - copy.addActionListener(this); - cut.setLabel("Cut"); - cut.addActionListener(this); - delete.setLabel("Delete"); - delete.addActionListener(this); - pasteMenu.setLabel("Paste"); - pasteNew.setLabel("To New Alignment"); - pasteNew.addActionListener(this); - pasteThis.setLabel("Add To This Alignment"); - pasteThis.addActionListener(this); - applyToAllGroups.setLabel("Apply Colour To All Groups"); - applyToAllGroups.setState(true); - applyToAllGroups.addItemListener(this); - font.setLabel("Font..."); - font.addActionListener(this); - scaleAbove.setLabel("Scale Above"); - scaleAbove.setState(true); - scaleAbove.setEnabled(false); - scaleAbove.addItemListener(this); - scaleLeft.setEnabled(false); - scaleLeft.setState(true); - scaleLeft.setLabel("Scale Left"); - scaleLeft.addItemListener(this); - scaleRight.setEnabled(false); - scaleRight.setState(true); - scaleRight.setLabel("Scale Right"); - scaleRight.addItemListener(this); - modifyPID.setLabel("Modify Identity Threshold..."); - modifyPID.addActionListener(this); - modifyConservation.setLabel("Modify Conservation Threshold..."); - modifyConservation.addActionListener(this); - sortByTreeMenu.setLabel("By Tree Order"); - sort.setLabel("Sort"); - calculate.setLabel("Calculate Tree"); - autoCalculate.addItemListener(this); - inputText.setLabel("Input from textbox"); - inputText.addActionListener(this); - - helpMenu.setLabel("Help"); - documentation.setLabel("Documentation"); - documentation.addActionListener(this); - - about.setLabel("About..."); - about.addActionListener(this); - seqLimits.setState(true); - seqLimits.setLabel("Show Sequence Limits"); - seqLimits.addItemListener(this); - featureSettings.setLabel("Feature Settings..."); - featureSettings.addActionListener(this); - sequenceFeatures.setLabel("Sequence Features"); - sequenceFeatures.addItemListener(this); - sequenceFeatures.setState(false); - annotationColour.setLabel("by Annotation..."); - annotationColour.addActionListener(this); - invertSequenceMenuItem.setLabel("Invert Sequence Selection"); - invertColSel.setLabel("Invert Column Selection"); - menu1.setLabel("Show"); - showColumns.setLabel("All Columns "); - showSeqs.setLabel("All Sequences"); - menu2.setLabel("Hide"); - hideColumns.setLabel("Selected Columns"); - hideSequences.setLabel("Selected Sequences"); - invertColSel.addActionListener(this); - showColumns.addActionListener(this); - showSeqs.addActionListener(this); - hideColumns.addActionListener(this); - hideSequences.addActionListener(this); - - - alignFrameMenuBar.add(fileMenu); - alignFrameMenuBar.add(editMenu); - alignFrameMenuBar.add(searchMenu); - alignFrameMenuBar.add(viewMenu); - alignFrameMenuBar.add(colourMenu); - alignFrameMenuBar.add(calculateMenu); - alignFrameMenuBar.add(helpMenu); - fileMenu.add(inputText); - fileMenu.add(outputTextboxMenu); - if(jalviewServletURL!=null) - fileMenu.add(loadApplication); - fileMenu.addSeparator(); - fileMenu.add(loadTree); - fileMenu.add(closeMenuItem); - editMenu.add(undoMenuItem); - editMenu.add(redoMenuItem); - editMenu.add(cut); - editMenu.add(copy); - editMenu.add(pasteMenu); - editMenu.add(delete); - editMenu.addSeparator(); - editMenu.add(selectAllSequenceMenuItem); - editMenu.add(deselectAllSequenceMenuItem); - editMenu.add(invertSequenceMenuItem); - editMenu.add(invertColSel); - editMenu.add(deleteGroups); - editMenu.addSeparator(); - editMenu.add(remove2LeftMenuItem); - editMenu.add(remove2RightMenuItem); - editMenu.add(removeGappedColumnMenuItem); - editMenu.add(removeAllGapsMenuItem); - editMenu.add(removeRedundancyMenuItem); - searchMenu.add(findMenuItem); - viewMenu.add(font); - viewMenu.addSeparator(); - viewMenu.add(menu1); - viewMenu.add(menu2); - viewMenu.addSeparator(); - viewMenu.add(wrapMenuItem); - viewMenu.add(scaleAbove); - viewMenu.add(scaleLeft); - viewMenu.add(scaleRight); - viewMenu.addSeparator(); - viewMenu.add(seqLimits); - viewMenu.add(viewBoxesMenuItem); - viewMenu.add(viewTextMenuItem); - viewMenu.add(colourTextMenuItem); - viewMenu.add(renderGapsMenuItem); - viewMenu.add(annotationPanelMenuItem); - viewMenu.addSeparator(); - viewMenu.add(sequenceFeatures); - viewMenu.add(featureSettings); - viewMenu.addSeparator(); - viewMenu.add(overviewMenuItem); - colourMenu.add(applyToAllGroups); - colourMenu.addSeparator(); - colourMenu.add(noColourmenuItem); - colourMenu.add(clustalColour); - colourMenu.add(BLOSUM62Colour); - colourMenu.add(PIDColour); - colourMenu.add(zappoColour); - colourMenu.add(taylorColour); - colourMenu.add(hydrophobicityColour); - colourMenu.add(helixColour); - colourMenu.add(strandColour); - colourMenu.add(turnColour); - colourMenu.add(buriedColour); - colourMenu.add(nucleotideColour); - colourMenu.add(userDefinedColour); - colourMenu.addSeparator(); - colourMenu.add(conservationMenuItem); - colourMenu.add(modifyConservation); - colourMenu.add(abovePIDThreshold); - colourMenu.add(modifyPID); - colourMenu.add(annotationColour); - calculateMenu.add(sort); - calculateMenu.add(calculate); - calculateMenu.addSeparator(); - calculateMenu.add(pairwiseAlignmentMenuItem); - calculateMenu.add(PCAMenuItem); - calculateMenu.add(autoCalculate); - this.add(statusBar, BorderLayout.SOUTH); - pasteMenu.add(pasteNew); - pasteMenu.add(pasteThis); - sort.add(sortIDMenuItem); - sort.add(sortByTreeMenu); - sort.add(sortGroupMenuItem); - sort.add(sortPairwiseMenuItem); - calculate.add(averageDistanceTreeMenuItem); - calculate.add(neighbourTreeMenuItem); - calculate.add(avDistanceTreeBlosumMenuItem); - calculate.add(njTreeBlosumMenuItem); - helpMenu.add(documentation); - helpMenu.add(about); - menu1.add(showColumns); - menu1.add(showSeqs); - menu2.add(hideColumns); - menu2.add(hideSequences); - } - - public void setEmbedded() - { - - embeddedMenu = new Panel(); - embeddedEdit = new Label(); - embeddedSearch = new Label(); - embeddedView = new Label(); - embeddedColour = new Label(); - embeddedFile = new Label(); - embeddedHelp = new Label(); - embeddedCalculate = new Label(); - flowLayout1 = new FlowLayout(); - embeddedMenu.setBackground(Color.lightGray); - embeddedMenu.setLayout(flowLayout1); - embeddedEdit.setText("Edit"); - embeddedEdit.setFont(new java.awt.Font("Arial", Font.PLAIN, 10)); - embeddedSearch.setText("Search"); - embeddedSearch.setFont(new java.awt.Font("Arial", Font.PLAIN, 10)); - embeddedView.setText("View"); - embeddedView.setFont(new java.awt.Font("Arial", Font.PLAIN, 10)); - embeddedColour.setText("Colour"); - embeddedColour.setFont(new java.awt.Font("Arial", Font.PLAIN, 10)); - embeddedFile.setFont(new java.awt.Font("Arial", Font.PLAIN, 10)); - embeddedFile.setText("File"); - embeddedHelp.setFont(new java.awt.Font("Arial", Font.PLAIN, 10)); - embeddedHelp.setText("Help"); - embeddedCalculate.setFont(new java.awt.Font("Arial", Font.PLAIN, 10)); - embeddedCalculate.setText("Calculate"); - embeddedMenu.add(embeddedFile); - embeddedMenu.add(embeddedEdit); - embeddedMenu.add(embeddedSearch); - embeddedMenu.add(embeddedView); - embeddedMenu.add(embeddedColour); - embeddedMenu.add(embeddedCalculate); - embeddedMenu.add(embeddedHelp); - flowLayout1.setAlignment(FlowLayout.LEFT); - flowLayout1.setHgap(2); - flowLayout1.setVgap(0); - embeddedFile.addMouseListener(this); - embeddedEdit.addMouseListener(this); - embeddedSearch.addMouseListener(this); - embeddedView.addMouseListener(this); - embeddedColour.addMouseListener(this); - embeddedCalculate.addMouseListener(this); - embeddedHelp.addMouseListener(this); - - // setVisible(false); - fileMenu.remove(closeMenuItem); - fileMenu.remove(3); // Seperator - - viewport.applet.setLayout(new BorderLayout()); - viewport.applet.add(embeddedMenu, BorderLayout.NORTH); - viewport.applet.add(statusBar, BorderLayout.SOUTH); - // viewport.applet.validate(); - - alignPanel.setSize(viewport.applet.size().width, viewport.applet.size().height - - embeddedMenu.HEIGHT - statusBar.HEIGHT); - - viewport.applet.add(alignPanel, BorderLayout.CENTER); - viewport.applet.validate(); - - } - - - - PopupMenu filePopup, editPopup, searchPopup, - viewPopup, colourPopup, calculatePopup, helpPopup; - MenuItem featureSettings = new MenuItem(); - CheckboxMenuItem sequenceFeatures = new CheckboxMenuItem(); - MenuItem annotationColour = new MenuItem(); - MenuItem invertColSel = new MenuItem(); - Menu menu1 = new Menu(); - MenuItem showColumns = new MenuItem(); - MenuItem showSeqs = new MenuItem(); - Menu menu2 = new Menu(); - MenuItem hideColumns = new MenuItem(); - MenuItem hideSequences = new MenuItem(); - - public void mousePressed(MouseEvent evt) - { - PopupMenu popup = null; - Label source = (Label)evt.getSource(); - if(source==embeddedFile) - { - popup = filePopup = genPopupMenu(filePopup, fileMenu); - } - else if(source==embeddedEdit) - { - popup = editPopup = genPopupMenu(editPopup, editMenu); - } - else if(source==embeddedSearch) - { - popup = searchPopup = genPopupMenu(searchPopup, searchMenu); - } - else if(source==embeddedView) - { - popup = viewPopup = genPopupMenu(viewPopup, viewMenu); - } - else if(source==embeddedColour) - { - popup = colourPopup = genPopupMenu(colourPopup, colourMenu); - } - else if(source==embeddedCalculate) - { - popup = calculatePopup = genPopupMenu(calculatePopup, calculateMenu); - } - else if(source==embeddedHelp) - { - popup = helpPopup = genPopupMenu(helpPopup, helpMenu); - } - - embeddedMenu.add(popup); - popup.show(embeddedMenu, - source.getBounds().x, - source.getBounds().y + source.getBounds().getSize().height); - } - - PopupMenu genPopupMenu(PopupMenu popup, Menu original) - { - if(popup!=null) - { - return popup; - } - popup = new PopupMenu(); - int m, mSize = original.getItemCount(); - for(m=0; m0) + alignPanel.seqPanel.seqCanvas + .getFeatureRenderer().featureLinks = featureLinks; + viewport.showSequenceFeatures = true; + sequenceFeatures.setState(true); + alignPanel.repaint(); + } + + } + + + public void keyPressed(KeyEvent evt) + { + if (viewport.cursorMode + && evt.getKeyCode() >= KeyEvent.VK_0 + && evt.getKeyCode() <= KeyEvent.VK_9) + { + alignPanel.seqPanel.numberPressed(evt.getKeyChar()); + } + + switch (evt.getKeyCode()) + { + case 27: // escape key + deselectAllSequenceMenuItem_actionPerformed(); + break; + case KeyEvent.VK_X: + if (evt.isControlDown() || evt.isMetaDown()) + { + cut_actionPerformed(); + } + break; + case KeyEvent.VK_C: + if (viewport.cursorMode && !evt.isControlDown()) + { + alignPanel.seqPanel.setCursorColumn(); + } + if (evt.isControlDown() || evt.isMetaDown()) + { + copy_actionPerformed(); + } + break; + case KeyEvent.VK_V: + if (evt.isControlDown() || evt.isMetaDown()) + { + paste(true); + } + break; + case KeyEvent.VK_A: + if (evt.isControlDown() || evt.isMetaDown()) + { + selectAllSequenceMenuItem_actionPerformed(); + } + break; + case KeyEvent.VK_DOWN: + if(viewport.cursorMode) + { + alignPanel.seqPanel.moveCursor(0,1); + } + else + moveSelectedSequences(false); + break; + + case KeyEvent.VK_UP: + if (viewport.cursorMode) + { + alignPanel.seqPanel.moveCursor(0,-1); + } + else + moveSelectedSequences(true); + break; + + case KeyEvent.VK_LEFT: + if(viewport.cursorMode) + { + alignPanel.seqPanel.moveCursor(-1,0); + } + break; + + case KeyEvent.VK_RIGHT: + if (viewport.cursorMode) + { + alignPanel.seqPanel.moveCursor(1,0); + } + break; + case KeyEvent.VK_SPACE: + if(viewport.cursorMode) + { + alignPanel.seqPanel.insertGapAtCursor(evt.isControlDown()); + } + break; + + case KeyEvent.VK_DELETE: + case KeyEvent.VK_BACK_SPACE: + if(viewport.cursorMode) + { + alignPanel.seqPanel.deleteGapAtCursor(evt.isControlDown()); + } + else + { + cut_actionPerformed(); + alignPanel.seqPanel.seqCanvas.repaint(); + } + break; + + case KeyEvent.VK_S: + if(viewport.cursorMode) + { + alignPanel.seqPanel.setCursorRow(); + } + break; + case KeyEvent.VK_P: + if(viewport.cursorMode) + { + alignPanel.seqPanel.setCursorPosition(); + } + break; + + case KeyEvent.VK_ENTER: + case KeyEvent.VK_COMMA: + if(viewport.cursorMode) + { + alignPanel.seqPanel.setCursorRowAndColumn(); + } + break; + + case KeyEvent.VK_Q: + if(viewport.cursorMode) + { + alignPanel.seqPanel.setSelectionAreaAtCursor(true); + } + break; + case KeyEvent.VK_M: + if(viewport.cursorMode) + { + alignPanel.seqPanel.setSelectionAreaAtCursor(false); + } + break; + + case KeyEvent.VK_F2: + viewport.cursorMode = ! viewport.cursorMode; + statusBar.setText("Keyboard editing mode is "+ + (viewport.cursorMode ? "on" : "off")); + if(viewport.cursorMode) + { + alignPanel.seqPanel.seqCanvas.cursorX = viewport.startRes; + alignPanel.seqPanel.seqCanvas.cursorY = viewport.startSeq; + } + alignPanel.seqPanel.seqCanvas.repaint(); + break; + + case KeyEvent.VK_F: + if (evt.isControlDown()) + { + findMenuItem_actionPerformed(); + } + break; + case KeyEvent.VK_H: + { + boolean toggleSeqs = !evt.isControlDown(); + boolean toggleCols = !evt.isShiftDown(); + boolean hide = false; + SequenceGroup sg = viewport.getSelectionGroup(); + + if(toggleSeqs) + { + if (sg != null && sg.getSize(false) != 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(); + } + + alignPanel.repaint(); + break; + } + + } + } + public void keyReleased(KeyEvent evt) + {} + public void keyTyped(KeyEvent evt) + {} + +public void itemStateChanged(ItemEvent evt) + { + if(evt.getSource()==colourTextMenuItem) + colourTextMenuItem_actionPerformed(); + else if(evt.getSource()==wrapMenuItem) + wrapMenuItem_actionPerformed(); + else if(evt.getSource()==scaleAbove) + scaleAbove_actionPerformed(); + else if(evt.getSource()==scaleLeft) + scaleLeft_actionPerformed(); + else if(evt.getSource()==scaleRight) + scaleRight_actionPerformed(); + else if(evt.getSource()==seqLimits) + seqLimits_itemStateChanged(); + else if(evt.getSource()==viewBoxesMenuItem) + viewBoxesMenuItem_actionPerformed(); + else if(evt.getSource()==viewTextMenuItem) + viewTextMenuItem_actionPerformed(); + else if(evt.getSource()==renderGapsMenuItem) + renderGapsMenuItem_actionPerformed(); + else if(evt.getSource()==annotationPanelMenuItem) + annotationPanelMenuItem_actionPerformed(); + else if(evt.getSource()==sequenceFeatures) + { + viewport.showSequenceFeatures(sequenceFeatures.getState()); + alignPanel.seqPanel.seqCanvas.repaint(); + } + else if(evt.getSource()==conservationMenuItem) + conservationMenuItem_actionPerformed(); + else if(evt.getSource()==abovePIDThreshold) + abovePIDThreshold_actionPerformed(); + else if(evt.getSource()==applyToAllGroups) + applyToAllGroups_actionPerformed(); + else if(evt.getSource()==autoCalculate) + viewport.autocalculateConsensus = autoCalculate.getState(); + } + public void actionPerformed(ActionEvent evt) + { + Object source = evt.getSource(); + + if(source==inputText) + inputText_actionPerformed(); + else if(source==loadTree) + loadTree_actionPerformed(); + else if(source==loadApplication) + launchFullApplication(); + else if(source==closeMenuItem) + closeMenuItem_actionPerformed(); + else if(source==copy) + copy_actionPerformed(); + else if(source==undoMenuItem) + undoMenuItem_actionPerformed(); + else if(source==redoMenuItem) + redoMenuItem_actionPerformed(); + else if(source==inputText) + inputText_actionPerformed(); + else if(source==closeMenuItem) + closeMenuItem_actionPerformed(); + else if(source==undoMenuItem) + undoMenuItem_actionPerformed(); + else if(source==redoMenuItem) + redoMenuItem_actionPerformed(); + else if(source==copy) + copy_actionPerformed(); + else if(source==pasteNew) + pasteNew_actionPerformed(); + else if(source==pasteThis) + pasteThis_actionPerformed(); + else if(source==cut) + cut_actionPerformed(); + else if(source==delete) + delete_actionPerformed(); + else if(source==deleteGroups) + deleteGroups_actionPerformed(); + else if(source==selectAllSequenceMenuItem) + selectAllSequenceMenuItem_actionPerformed(); + else if(source==deselectAllSequenceMenuItem) + deselectAllSequenceMenuItem_actionPerformed(); + else if(source==invertSequenceMenuItem) + invertSequenceMenuItem_actionPerformed(); + else if(source==invertColSel) + { viewport.invertColumnSelection(); alignPanel.repaint(); } + else if(source==remove2LeftMenuItem) + remove2LeftMenuItem_actionPerformed(); + else if(source==remove2RightMenuItem) + remove2RightMenuItem_actionPerformed(); + else if(source==removeGappedColumnMenuItem) + removeGappedColumnMenuItem_actionPerformed(); + else if(source==removeAllGapsMenuItem) + removeAllGapsMenuItem_actionPerformed(); + else if(source==findMenuItem) + findMenuItem_actionPerformed(); + else if(source==font) + font_actionPerformed(); + else if(source==showColumns) + { + viewport.showAllHiddenColumns(); alignPanel.repaint(); + } + else if(source==showSeqs) + { + viewport.showAllHiddenSeqs(); + } + else if(source == hideColumns) + { + viewport.hideSelectedColumns(); alignPanel.repaint(); + } + else if(source == hideSequences && viewport.getSelectionGroup()!=null) + { + viewport.hideAllSelectedSeqs(); + } + else if(source==featureSettings) + featureSettings_actionPerformed(); + else if(source==overviewMenuItem) + overviewMenuItem_actionPerformed(); + else if(source==noColourmenuItem) + noColourmenuItem_actionPerformed(); + else if(source==clustalColour) + clustalColour_actionPerformed(); + else if(source==zappoColour) + zappoColour_actionPerformed(); + else if(source==taylorColour) + taylorColour_actionPerformed(); + else if(source==hydrophobicityColour) + hydrophobicityColour_actionPerformed(); + else if(source==helixColour) + helixColour_actionPerformed(); + else if(source==strandColour) + strandColour_actionPerformed(); + else if(source==turnColour) + turnColour_actionPerformed(); + else if(source==buriedColour) + buriedColour_actionPerformed(); + else if(source==nucleotideColour) + nucleotideColour_actionPerformed(); + else if(source==modifyPID) + modifyPID_actionPerformed(); + else if(source==modifyConservation) + modifyConservation_actionPerformed(); + else if(source==userDefinedColour) + userDefinedColour_actionPerformed(); + else if(source==PIDColour) + PIDColour_actionPerformed(); + else if(source==BLOSUM62Colour) + BLOSUM62Colour_actionPerformed(); + else if(source==annotationColour) + new AnnotationColourChooser(viewport, alignPanel); + else if(source==sortPairwiseMenuItem) + sortPairwiseMenuItem_actionPerformed(); + else if(source==sortIDMenuItem) + sortIDMenuItem_actionPerformed(); + else if(source==sortGroupMenuItem) + sortGroupMenuItem_actionPerformed(); + else if(source==removeRedundancyMenuItem) + removeRedundancyMenuItem_actionPerformed(); + else if(source==pairwiseAlignmentMenuItem) + pairwiseAlignmentMenuItem_actionPerformed(); + else if(source==PCAMenuItem) + PCAMenuItem_actionPerformed(); + else if(source==averageDistanceTreeMenuItem) + averageDistanceTreeMenuItem_actionPerformed(); + else if(source==neighbourTreeMenuItem) + neighbourTreeMenuItem_actionPerformed(); + else if(source==njTreeBlosumMenuItem) + njTreeBlosumMenuItem_actionPerformed(); + else if(source==avDistanceTreeBlosumMenuItem) + avTreeBlosumMenuItem_actionPerformed(); + else if(source==documentation) + documentation_actionPerformed(); + else if(source==about) + about_actionPerformed(); + + } + + public void inputText_actionPerformed() + { + CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this); + Frame frame = new Frame(); + frame.add(cap); + jalview.bin.JalviewLite.addFrame(frame, "Cut & Paste Input", 500, 500); + } + + protected void outputText_actionPerformed(ActionEvent e) + { + CutAndPasteTransfer cap = new CutAndPasteTransfer(false, this); + Frame frame = new Frame(); + frame.add(cap); + jalview.bin.JalviewLite.addFrame(frame, + "Alignment output - " + e.getActionCommand(), + 600, 500); + cap.setText(new AppletFormatAdapter().formatSequences(e.getActionCommand(), + viewport.getAlignment().getSequences(), + viewport.showJVSuffix)); + } + + void launchFullApplication() + { + StringBuffer url = new StringBuffer(jalviewServletURL); + + url.append("?open="+ + appendProtocol( viewport.applet.getParameter("file") ) ); + + if(viewport.applet.getParameter("features")!=null) + { + url.append( "&features=" ); + url.append( appendProtocol( viewport.applet.getParameter("features") ) ); + } + + if(viewport.applet.getParameter("annotations")!=null) + { + url.append( "&annotations=" ); + url.append( appendProtocol( viewport.applet.getParameter("annotations") ) ); + } + + if(viewport.applet.getParameter("defaultColour")!=null) + { + url.append("&colour=" + + removeWhiteSpace(viewport.applet.getParameter("defaultColour")) + ); + } + + if(viewport.applet.getParameter("userDefinedColour")!=null) + { + url.append( "&colour=" + + removeWhiteSpace( viewport.applet.getParameter("userDefinedColour") ) + ); + } + + showURL(url.toString(), "FULL_APP"); + } + + + String removeWhiteSpace(String colour) + { + StringBuffer sb = new StringBuffer(); + for (int i = 0; i < colour.length(); i++) + { + if (Character.isWhitespace(colour.charAt(i))) + sb.append("%20"); + else + sb.append(colour.charAt(i)); + } + + return sb.toString(); + } + + + String appendProtocol(String url) + { + try{ + new URL(url); + }catch(java.net.MalformedURLException ex) + { + url = viewport.applet.getCodeBase()+url; + } + return url; + } + + public void closeMenuItem_actionPerformed() + { + PaintRefresher.components.remove(viewport.alignment); + if(PaintRefresher.components.size()==0 && viewport.applet==null) + System.exit(0); + + this.dispose(); + } + + Stack historyList = new Stack(); + Stack redoList = new Stack(); + + void updateEditMenuBar() + { + if (historyList.size() > 0) + { + undoMenuItem.setEnabled(true); + HistoryItem hi = (HistoryItem) historyList.peek(); + undoMenuItem.setLabel("Undo " + hi.getDescription()); + } + else + { + undoMenuItem.setEnabled(false); + undoMenuItem.setLabel("Undo"); + } + + if (redoList.size() > 0) + { + redoMenuItem.setEnabled(true); + HistoryItem hi = (HistoryItem) redoList.peek(); + redoMenuItem.setLabel("Redo " + hi.getDescription()); + } + else + { + redoMenuItem.setEnabled(false); + redoMenuItem.setLabel("Redo"); + } + } + + public void addHistoryItem(HistoryItem hi) + { + historyList.push(hi); + redoList.removeAllElements(); + updateEditMenuBar(); + } + + protected void undoMenuItem_actionPerformed() + { + HistoryItem nh,hi = (HistoryItem) historyList.pop(); + redoList.push(nh=new HistoryItem(hi.getDescription(), viewport.alignment, + HistoryItem.HIDE)); + if (hi.alColumnChanges!=null) + nh.alColumnChanges=hi.alColumnChanges.getInverse(); + restoreHistoryItem(hi); + viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences()); + } + + protected void redoMenuItem_actionPerformed() + { + HistoryItem nh,hi = (HistoryItem) redoList.pop(); + historyList.push(nh=new HistoryItem(hi.getDescription(), viewport.alignment, + HistoryItem.HIDE)); + if (hi.alColumnChanges!=null) + nh.alColumnChanges=hi.alColumnChanges.getInverse(); + restoreHistoryItem(hi); + updateEditMenuBar(); + viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences()); + } + + // used by undo and redo + void restoreHistoryItem(HistoryItem hi) + { + hi.restore(viewport.getColumnSelection()); + updateEditMenuBar(); + + viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences()); + } + + 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(false).contains(seq)) + { + continue; + } + + SequenceI temp = viewport.alignment.getSequenceAt(i - 1); + if (sg.getSequences(false).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(true).contains(seq)) + { + continue; + } + + SequenceI temp = viewport.alignment.getSequenceAt(i + 1); + if (sg.getSequences(true).contains(temp)) + { + continue; + } + + viewport.alignment.getSequences().setElementAt(temp, i); + viewport.alignment.getSequences().setElementAt(seq, i + 1); + } + } + + alignPanel.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(false); 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(false); 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.getSequence(sg.getStartRes(), + sg.getEndRes() + 1) + "\n"); + } + + } + + protected void pasteNew_actionPerformed() + { + paste(true); + } + + protected void pasteThis_actionPerformed() + { + addHistoryItem(new HistoryItem("Paste Sequences", viewport.alignment, + HistoryItem.PASTE)); + 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()); + Sequence sequence = new Sequence(name, st.nextToken(), start, end); + + if (!newAlignment) + { + viewport.alignment.addSequence(sequence); + } + else + { + seqs.addElement(sequence); + } + } + + if (newAlignment) + { + SequenceI[] newSeqs = new SequenceI[seqs.size()]; + for (int i = 0; i < seqs.size(); i++) + { + newSeqs[i] = (SequenceI) seqs.elementAt(i); + } + + 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, NEW_WINDOW_WIDTH, + NEW_WINDOW_HEIGHT); + } + else + { + viewport.setEndSeq(viewport.alignment.getHeight()); + viewport.alignment.getWidth(); + viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences()); + } + + } + catch (Exception ex) + {} // could be anything being pasted in here + + } + + protected void cut_actionPerformed() + { + copy_actionPerformed(); + delete_actionPerformed(); + } + + protected void delete_actionPerformed() + { + addHistoryItem(new HistoryItem("Delete Sequences", viewport.alignment, + HistoryItem.HIDE)); + if (viewport.getSelectionGroup() == null) + { + return; + } + + + SequenceGroup sg = viewport.getSelectionGroup(); + boolean allSequences = false; + if(sg.getSize(false)==viewport.alignment.getHeight()) + allSequences = true; + + for (int i = 0; i < sg.getSize(false); i++) + { + SequenceI seq = sg.getSequenceAt(i); + int index = viewport.getAlignment().findIndex(seq); + seq.deleteChars(sg.getStartRes(), sg.getEndRes() + 1); + + // If the cut affects all sequences, remove highlighted columns + if (allSequences) + { + viewport.getColumnSelection().removeElements(sg.getStartRes(), + sg.getEndRes() + 1); + } + + + if (seq.getSequence().length() < 1) + { + viewport.getAlignment().deleteSequence(seq); + } + else + { + viewport.getAlignment().getSequences().setElementAt(seq, index); + } + } + + viewport.setSelectionGroup(null); + viewport.alignment.deleteGroup(sg); + viewport.resetSeqLimits(alignPanel.seqPanel.seqCanvas.getSize().height); + if (viewport.getAlignment().getHeight() < 1) + { + try + { + this.setVisible(false); + } + catch (Exception ex) + {} + } + viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences()); + + } + + protected void deleteGroups_actionPerformed() + { + viewport.alignment.deleteAllGroups(); + viewport.setSelectionGroup(null); + + alignPanel.repaint(); + } + + 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.repaint(); + PaintRefresher.Refresh(null, viewport.alignment); + } + + public void deselectAllSequenceMenuItem_actionPerformed() + { + if(viewport.cursorMode) + { + alignPanel.seqPanel.keyboardNo1=null; + alignPanel.seqPanel.keyboardNo2=null; + } + viewport.setSelectionGroup(null); + viewport.getColumnSelection().clear(); + viewport.setSelectionGroup(null); + alignPanel.idPanel.idCanvas.searchResults = null; + alignPanel.seqPanel.seqCanvas.highlightSearchResults(null); + alignPanel.repaint(); + PaintRefresher.Refresh(null, viewport.alignment); + } + + public void invertSequenceMenuItem_actionPerformed() + { + SequenceGroup sg = viewport.getSelectionGroup(); + for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++) + { + sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false); + } + + PaintRefresher.Refresh(null, viewport.alignment); + } + + public void remove2LeftMenuItem_actionPerformed() + { + ColumnSelection colSel = viewport.getColumnSelection(); + if (colSel.size() > 0) + { + HistoryItem edit; + addHistoryItem(edit=new HistoryItem("Remove Left", viewport.alignment, + HistoryItem.HIDE)); + int min = colSel.getMin(); + viewport.getAlignment().trimLeft(min); + colSel.compensateForEdit(0, min); + edit.addShift(0, min); + if (viewport.getSelectionGroup() != null) + { + viewport.getSelectionGroup().adjustForRemoveLeft(min); + } + + Vector groups = viewport.alignment.getGroups(); + for (int i = 0; i < groups.size(); i++) + { + SequenceGroup sg = (SequenceGroup) groups.elementAt(i); + if (!sg.adjustForRemoveLeft(min)) + { + viewport.alignment.deleteGroup(sg); + } + } + viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences()); + } + } + + public void remove2RightMenuItem_actionPerformed() + { + ColumnSelection colSel = viewport.getColumnSelection(); + if (colSel.size() > 0) + { + addHistoryItem(new HistoryItem("Remove Right", viewport.alignment, + HistoryItem.HIDE)); + int max = colSel.getMax(); + viewport.getAlignment().trimRight(max); + + if (viewport.getSelectionGroup() != null) + { + viewport.getSelectionGroup().adjustForRemoveRight(max); + } + + Vector groups = viewport.alignment.getGroups(); + for (int i = 0; i < groups.size(); i++) + { + SequenceGroup sg = (SequenceGroup) groups.elementAt(i); + if (!sg.adjustForRemoveRight(max)) + { + viewport.alignment.deleteGroup(sg); + } + } + viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences()); + } + + } + + public void removeGappedColumnMenuItem_actionPerformed() + { + HistoryItem edit; + addHistoryItem(edit=new HistoryItem("Remove Gapped Columns", + viewport.alignment, + HistoryItem.HIDE)); + + //This is to maintain viewport position on first residue + //of first sequence + SequenceI seq = viewport.alignment.getSequenceAt(0); + int startRes = seq.findPosition(viewport.startRes); + + viewport.getAlignment().removeGaps(); + + viewport.setStartRes(seq.findIndex(startRes)-1); + + viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences()); + } + + public void removeAllGapsMenuItem_actionPerformed() + { + // TODO: hidden regions should not be touched by removeAllGaps - a minimal number of gaps will remain in alignment segments containing uneven length subsequences + // TODO: columnSelection.compensateforedits should be called (and passed to history item) + HistoryItem editgaps; + addHistoryItem(editgaps=new HistoryItem("Remove Gaps", viewport.alignment, + HistoryItem.HIDE)); + + //This is to maintain viewport position on first residue + //of first sequence + SequenceI seq = viewport.alignment.getSequenceAt(0); + int startRes = seq.findPosition(viewport.startRes); + + SequenceI current; + Vector seqs=null; + + int start=0, end = viewport.alignment.getWidth(); + + if (viewport.getSelectionGroup() != null + && viewport.getSelectionGroup().getSequences(false) != null + && viewport.getSelectionGroup().getSize(false)>0) + { + seqs = viewport.getSelectionGroup().getSequences(true); + start = viewport.getSelectionGroup().getStartRes(); + end = viewport.getSelectionGroup().getEndRes()+1; + } + else + seqs = viewport.alignment.getSequences(); + + /* Commented out regions below are partial implementation of todo above. + * divide start,end into visible chunks, and for each: + int diff=end-start+1; + int diffmax=0; + int dr[] = new int[seqs.size()]; + */ + for (int i = 0; i < seqs.size(); i++) + { + current = (SequenceI) seqs.elementAt(i); + //dr[i]= + current.removeGaps(start, end); + /*if (d0) { + // record shift for history. + editgaps.addShift(start, diff); + if (viewport.hasHiddenColumns && diffmax>diff) { + // pad sequence + StringBuffer gaps=new StringBuffer(diffmax); + for (int i=0,j=diffmax-diff; i0) { + String sq = current.getSequence(); + current.setSequence(sq.substring(0, hcend-dr[i])+gaps.substring(0, dr[i]-diff)+sq.substring()); + } + } + } + }*/ + + viewport.setStartRes(seq.findIndex(startRes)-1); + viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences()); + } + + public void alignmentChanged() + { + viewport.alignment.padGaps(); + if(viewport.autocalculateConsensus) + { + viewport.updateConsensus(); + viewport.updateConservation(); + } + + resetAllColourSchemes(); + if(alignPanel.overviewPanel!=null) + alignPanel.overviewPanel.updateOverviewImage(); + + viewport.alignment.adjustSequenceAnnotations(); + alignPanel.repaint(); + } + + void resetAllColourSchemes() + { + ColourSchemeI cs = viewport.globalColourScheme; + if(cs!=null) + { + if (cs instanceof ClustalxColourScheme) + { + ( (ClustalxColourScheme) viewport.getGlobalColourScheme()). + resetClustalX(viewport.alignment.getSequences(), + viewport.alignment.getWidth()); + } + + cs.setConsensus(viewport.vconsensus); + if (cs.conservationApplied()) + { + 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); + } + } + + int s, sSize = viewport.alignment.getGroups().size(); + for(s=0; s 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()) + { + SequenceI current; + int Width = viewport.getAlignment().getWidth(); + + for (int i = 0; i < viewport.getAlignment().getSequences().size(); + i++) + { + current = viewport.getAlignment().getSequenceAt(i); + + if (current.getLength() < Width) + { + current.insertCharAt(Width - 1, viewport.getGapCharacter()); + } + } + alignPanel.repaint(); + } + + if ( (viewport.getSelectionGroup() != null && + viewport.getSelectionGroup().getSize(false) < 4 && + viewport.getSelectionGroup().getSize(false) > 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 BLOSUM62PID"); + } + + void NewTreePanel(String type, String pwType, String title) + { + //are the sequences aligned? + if (!viewport.alignment.isAligned()) + { + SequenceI current; + int Width = viewport.getAlignment().getWidth(); + + for (int i = 0; i < viewport.getAlignment().getSequences().size(); + i++) + { + current = viewport.getAlignment().getSequenceAt(i); + + if (current.getLength() < Width) + { + current.insertCharAt(Width - 1, viewport.getGapCharacter()); + } + } + alignPanel.repaint(); + + } + + if ( (viewport.getSelectionGroup() != null && + viewport.getSelectionGroup().getSize(false) > 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.treeImport = true; + Frame frame = new Frame(); + frame.add(cap); + jalview.bin.JalviewLite.addFrame(frame, "Paste Newick file ", 400, 300); + } + + public void loadTree(jalview.io.NewickFile tree, String treeFile) + { + TreePanel tp = new TreePanel(viewport, + treeFile, + "From File - ", + tree); + jalview.bin.JalviewLite.addFrame(tp, treeFile, 600, 500); + addTreeMenuItem(tp, treeFile); + } + + void addTreeMenuItem(final TreePanel treePanel, String title) + { + final MenuItem item = new MenuItem(title); + sortByTreeMenu.add(item); + item.addActionListener(new java.awt.event.ActionListener() + { + public void actionPerformed(ActionEvent evt) + { + addHistoryItem(new HistoryItem("Sort", viewport.alignment, + HistoryItem.SORT)); + AlignmentSorter.sortByTree(viewport.getAlignment(), treePanel.getTree()); + alignPanel.repaint(); + } + }); + + treePanel.addWindowListener(new WindowAdapter() + { + 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; + public AboutPanel(String version) + { this.version = version; } + + 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); + g.setFont(new Font("Helvetica", Font.BOLD, 14)); + g.drawString("Jalview - Release "+version, 200, y += fh); + g.setFont(new Font("Helvetica", Font.PLAIN, 12)); + g.drawString("Authors: Michele Clamp, James Cuff, Steve Searle, Andrew Waterhouse, Jim Procter & Geoff Barton.", + x, y += fh * 2); + g.drawString("Current development managed by Andrew Waterhouse; Barton Group, University of Dundee.", + x, y += fh); + g.drawString( + "For any issues relating to Jalview, email help@jalview.org", x, + y += fh); + g.drawString("If you use JalView, please cite:", x, y += fh + 8); + g.drawString("\"Clamp, M., Cuff, J., Searle, S. M. and Barton, G. J. (2004), The Jalview Java Alignment Editor\"", + x, y += fh); + g.drawString("Bioinformatics, 2004 20;426-7.", x, y += fh); + } + } + + String version = "test"; + java.net.URL url = getClass().getResource("/.build_properties"); + if (url != null) + { + try + { + BufferedReader reader = new BufferedReader(new InputStreamReader( + url.openStream())); + String line; + while ( (line = reader.readLine()) != null) + { + if (line.indexOf("VERSION") > -1) + { + version = line.substring(line.indexOf("=") + 1); + } + } + } + catch (Exception ex) + { + ex.printStackTrace(); + } + } + + + Frame frame = new Frame(); + frame.add(new AboutPanel(version)); + jalview.bin.JalviewLite.addFrame(frame, "Jalview", 580, 200); + + } + + public void showURL(String url, String target) + { + if (viewport.applet == null) + { + System.out.println("Not running as applet - no browser available."); + } + else + { + try + { + System.out.println("Show url: "+url); + viewport.applet.getAppletContext().showDocument(new java.net.URL(url), + target); + } + catch (Exception ex) + { + ex.printStackTrace(); + } + } + } + + + ////////////////////////////////////////////////////////////////////////////////// + //JBuilder Graphics here + + protected MenuBar alignFrameMenuBar = new MenuBar(); + protected Menu fileMenu = new Menu("File"); + protected MenuItem loadApplication = new MenuItem("View in Full Application"); + protected MenuItem loadTree = new MenuItem("Load Associated Tree"); + protected MenuItem closeMenuItem = new MenuItem("Close"); + protected Menu editMenu = new Menu("Edit"); + protected Menu viewMenu = new Menu("View"); + protected Menu colourMenu = new Menu("Colour"); + protected Menu calculateMenu = new Menu("Calculate"); + protected MenuItem selectAllSequenceMenuItem = new MenuItem("Select all"); + protected MenuItem deselectAllSequenceMenuItem = new MenuItem("Deselect All"); + protected MenuItem invertSequenceMenuItem = new MenuItem("Invert Selection"); + protected MenuItem remove2LeftMenuItem = new MenuItem(); + protected MenuItem remove2RightMenuItem = new MenuItem(); + protected MenuItem removeGappedColumnMenuItem = new MenuItem(); + protected MenuItem removeAllGapsMenuItem = new MenuItem(); + protected CheckboxMenuItem viewBoxesMenuItem = new CheckboxMenuItem(); + protected CheckboxMenuItem viewTextMenuItem = new CheckboxMenuItem(); + protected MenuItem sortPairwiseMenuItem = new MenuItem(); + protected MenuItem sortIDMenuItem = new MenuItem(); + protected MenuItem sortGroupMenuItem = new MenuItem(); + protected MenuItem removeRedundancyMenuItem = new MenuItem(); + protected MenuItem pairwiseAlignmentMenuItem = new MenuItem(); + protected MenuItem PCAMenuItem = new MenuItem(); + protected MenuItem averageDistanceTreeMenuItem = new MenuItem(); + protected MenuItem neighbourTreeMenuItem = new MenuItem(); + BorderLayout borderLayout1 = new BorderLayout(); + public Label statusBar = new Label(); + protected Menu outputTextboxMenu = new Menu(); + protected MenuItem clustalColour = new MenuItem(); + protected MenuItem zappoColour = new MenuItem(); + protected MenuItem taylorColour = new MenuItem(); + protected MenuItem hydrophobicityColour = new MenuItem(); + protected MenuItem helixColour = new MenuItem(); + protected MenuItem strandColour = new MenuItem(); + protected MenuItem turnColour = new MenuItem(); + protected MenuItem buriedColour = new MenuItem(); + protected MenuItem userDefinedColour = new MenuItem(); + protected MenuItem PIDColour = new MenuItem(); + protected MenuItem BLOSUM62Colour = new MenuItem(); + MenuItem njTreeBlosumMenuItem = new MenuItem(); + MenuItem avDistanceTreeBlosumMenuItem = new MenuItem(); + protected CheckboxMenuItem annotationPanelMenuItem = new CheckboxMenuItem(); + protected CheckboxMenuItem colourTextMenuItem = new CheckboxMenuItem(); + MenuItem overviewMenuItem = new MenuItem(); + protected MenuItem undoMenuItem = new MenuItem(); + protected MenuItem redoMenuItem = new MenuItem(); + protected CheckboxMenuItem conservationMenuItem = new CheckboxMenuItem(); + MenuItem noColourmenuItem = new MenuItem(); + protected CheckboxMenuItem wrapMenuItem = new CheckboxMenuItem(); + protected CheckboxMenuItem renderGapsMenuItem = new CheckboxMenuItem(); + MenuItem findMenuItem = new MenuItem(); + Menu searchMenu = new Menu(); + protected CheckboxMenuItem abovePIDThreshold = new CheckboxMenuItem(); + protected MenuItem nucleotideColour = new MenuItem(); + MenuItem deleteGroups = new MenuItem(); + MenuItem delete = new MenuItem(); + MenuItem copy = new MenuItem(); + MenuItem cut = new MenuItem(); + Menu pasteMenu = new Menu(); + MenuItem pasteNew = new MenuItem(); + MenuItem pasteThis = new MenuItem(); + protected CheckboxMenuItem applyToAllGroups = new CheckboxMenuItem(); + protected MenuItem font = new MenuItem(); + protected CheckboxMenuItem scaleAbove = new CheckboxMenuItem(); + protected CheckboxMenuItem scaleLeft = new CheckboxMenuItem(); + protected CheckboxMenuItem scaleRight = new CheckboxMenuItem(); + MenuItem modifyPID = new MenuItem(); + MenuItem modifyConservation = new MenuItem(); + protected CheckboxMenuItem autoCalculate + = new CheckboxMenuItem("Autocalculate Consensus", true); + protected Menu sortByTreeMenu = new Menu(); + Menu sort = new Menu(); + Menu calculate = new Menu(); + MenuItem inputText = new MenuItem(); + Menu helpMenu = new Menu(); + MenuItem documentation = new MenuItem(); + MenuItem about = new MenuItem(); + protected CheckboxMenuItem seqLimits = new CheckboxMenuItem(); + Panel embeddedMenu; + Label embeddedEdit; + Label embeddedSearch; + Label embeddedView; + Label embeddedColour; + Label embeddedFile; + Label embeddedHelp; + Label embeddedCalculate; + FlowLayout flowLayout1; + + private void jbInit() throws Exception { + + setMenuBar(alignFrameMenuBar); + + MenuItem item; + + // dynamically fill save as menu with available formats + for (int i = 0; i < jalview.io.AppletFormatAdapter.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); + selectAllSequenceMenuItem.addActionListener(this); + deselectAllSequenceMenuItem.addActionListener(this); + invertSequenceMenuItem.addActionListener(this); + remove2LeftMenuItem.setLabel("Remove Left"); + remove2LeftMenuItem.addActionListener(this); + remove2RightMenuItem.setLabel("Remove Right"); + remove2RightMenuItem.addActionListener(this); + removeGappedColumnMenuItem.setLabel("Remove Empty Columns"); + removeGappedColumnMenuItem.addActionListener(this); + removeAllGapsMenuItem.setLabel("Remove All Gaps"); + removeAllGapsMenuItem.addActionListener(this); + viewBoxesMenuItem.setLabel("Boxes"); + viewBoxesMenuItem.setState(true); + viewBoxesMenuItem.addItemListener(this); + viewTextMenuItem.setLabel("Text"); + viewTextMenuItem.setState(true); + viewTextMenuItem.addItemListener(this); + sortPairwiseMenuItem.setLabel("by Pairwise Identity"); + sortPairwiseMenuItem.addActionListener(this); + sortIDMenuItem.setLabel("by ID"); + sortIDMenuItem.addActionListener(this); + sortGroupMenuItem.setLabel("by Group"); + sortGroupMenuItem.addActionListener(this); + removeRedundancyMenuItem.setLabel("Remove Redundancy..."); + removeRedundancyMenuItem.addActionListener(this); + pairwiseAlignmentMenuItem.setLabel("Pairwise Alignments..."); + pairwiseAlignmentMenuItem.addActionListener(this); + PCAMenuItem.setLabel("Principal Component Analysis"); + PCAMenuItem.addActionListener(this); + averageDistanceTreeMenuItem.setLabel( + "Average Distance Using % Identity"); + averageDistanceTreeMenuItem.addActionListener(this); + neighbourTreeMenuItem.setLabel("Neighbour Joining Using % Identity"); + neighbourTreeMenuItem.addActionListener(this); + alignFrameMenuBar.setFont(new java.awt.Font("Verdana", 0, 11)); + statusBar.setBackground(Color.white); + statusBar.setFont(new java.awt.Font("Verdana", 0, 11)); + statusBar.setText("Status bar"); + outputTextboxMenu.setLabel("Output to Textbox"); + clustalColour.setLabel("Clustalx"); + + clustalColour.addActionListener(this); + zappoColour.setLabel("Zappo"); + zappoColour.addActionListener(this); + taylorColour.setLabel("Taylor"); + taylorColour.addActionListener(this); + hydrophobicityColour.setLabel("Hydrophobicity"); + hydrophobicityColour.addActionListener(this); + helixColour.setLabel("Helix Propensity"); + helixColour.addActionListener(this); + strandColour.setLabel("Strand Propensity"); + strandColour.addActionListener(this); + turnColour.setLabel("Turn Propensity"); + turnColour.addActionListener(this); + buriedColour.setLabel("Buried Index"); + buriedColour.addActionListener(this); + userDefinedColour.setLabel("User Defined..."); + userDefinedColour.addActionListener(this); + PIDColour.setLabel("Percentage Identity"); + PIDColour.addActionListener(this); + BLOSUM62Colour.setLabel("BLOSUM62 Score"); + BLOSUM62Colour.addActionListener(this); + avDistanceTreeBlosumMenuItem.setLabel( + "Average Distance Using BLOSUM62"); + avDistanceTreeBlosumMenuItem.addActionListener(this); + njTreeBlosumMenuItem.setLabel("Neighbour Joining Using BLOSUM62"); + njTreeBlosumMenuItem.addActionListener(this); + annotationPanelMenuItem.setLabel("Show Annotations"); + annotationPanelMenuItem.addItemListener(this); + colourTextMenuItem.setLabel("Colour Text"); + colourTextMenuItem.addItemListener(this); + overviewMenuItem.setLabel("Overview Window"); + overviewMenuItem.addActionListener(this); + undoMenuItem.setEnabled(false); + undoMenuItem.setLabel("Undo"); + undoMenuItem.addActionListener(this); + redoMenuItem.setEnabled(false); + redoMenuItem.setLabel("Redo"); + redoMenuItem.addActionListener(this); + conservationMenuItem.setLabel("by Conservation"); + conservationMenuItem.addItemListener(this); + noColourmenuItem.setLabel("None"); + noColourmenuItem.addActionListener(this); + wrapMenuItem.setLabel("Wrap"); + wrapMenuItem.addItemListener(this); + renderGapsMenuItem.setLabel("Show Gaps"); + renderGapsMenuItem.setState(true); + renderGapsMenuItem.addItemListener(this); + findMenuItem.setLabel("Find..."); + findMenuItem.addActionListener(this); + searchMenu.setLabel("Search"); + + abovePIDThreshold.setLabel("Above Identity Threshold"); + abovePIDThreshold.addItemListener(this); + nucleotideColour.setLabel("Nucleotide"); + nucleotideColour.addActionListener(this); + deleteGroups.setLabel("Undefine Groups"); + deleteGroups.addActionListener(this); + copy.setLabel("Copy"); + copy.addActionListener(this); + cut.setLabel("Cut"); + cut.addActionListener(this); + delete.setLabel("Delete"); + delete.addActionListener(this); + pasteMenu.setLabel("Paste"); + pasteNew.setLabel("To New Alignment"); + pasteNew.addActionListener(this); + pasteThis.setLabel("Add To This Alignment"); + pasteThis.addActionListener(this); + applyToAllGroups.setLabel("Apply Colour To All Groups"); + applyToAllGroups.setState(true); + applyToAllGroups.addItemListener(this); + font.setLabel("Font..."); + font.addActionListener(this); + scaleAbove.setLabel("Scale Above"); + scaleAbove.setState(true); + scaleAbove.setEnabled(false); + scaleAbove.addItemListener(this); + scaleLeft.setEnabled(false); + scaleLeft.setState(true); + scaleLeft.setLabel("Scale Left"); + scaleLeft.addItemListener(this); + scaleRight.setEnabled(false); + scaleRight.setState(true); + scaleRight.setLabel("Scale Right"); + scaleRight.addItemListener(this); + modifyPID.setLabel("Modify Identity Threshold..."); + modifyPID.addActionListener(this); + modifyConservation.setLabel("Modify Conservation Threshold..."); + modifyConservation.addActionListener(this); + sortByTreeMenu.setLabel("By Tree Order"); + sort.setLabel("Sort"); + calculate.setLabel("Calculate Tree"); + autoCalculate.addItemListener(this); + inputText.setLabel("Input from textbox"); + inputText.addActionListener(this); + + helpMenu.setLabel("Help"); + documentation.setLabel("Documentation"); + documentation.addActionListener(this); + + about.setLabel("About..."); + about.addActionListener(this); + seqLimits.setState(true); + seqLimits.setLabel("Show Sequence Limits"); + seqLimits.addItemListener(this); + featureSettings.setLabel("Feature Settings..."); + featureSettings.addActionListener(this); + sequenceFeatures.setLabel("Sequence Features"); + sequenceFeatures.addItemListener(this); + sequenceFeatures.setState(false); + annotationColour.setLabel("by Annotation..."); + annotationColour.addActionListener(this); + invertSequenceMenuItem.setLabel("Invert Sequence Selection"); + invertColSel.setLabel("Invert Column Selection"); + menu1.setLabel("Show"); + showColumns.setLabel("All Columns "); + showSeqs.setLabel("All Sequences"); + menu2.setLabel("Hide"); + hideColumns.setLabel("Selected Columns"); + hideSequences.setLabel("Selected Sequences"); + invertColSel.addActionListener(this); + showColumns.addActionListener(this); + showSeqs.addActionListener(this); + hideColumns.addActionListener(this); + hideSequences.addActionListener(this); + + + alignFrameMenuBar.add(fileMenu); + alignFrameMenuBar.add(editMenu); + alignFrameMenuBar.add(searchMenu); + alignFrameMenuBar.add(viewMenu); + alignFrameMenuBar.add(colourMenu); + alignFrameMenuBar.add(calculateMenu); + alignFrameMenuBar.add(helpMenu); + fileMenu.add(inputText); + fileMenu.add(outputTextboxMenu); + if(jalviewServletURL!=null) + fileMenu.add(loadApplication); + fileMenu.addSeparator(); + fileMenu.add(loadTree); + fileMenu.add(closeMenuItem); + editMenu.add(undoMenuItem); + editMenu.add(redoMenuItem); + editMenu.add(cut); + editMenu.add(copy); + editMenu.add(pasteMenu); + editMenu.add(delete); + editMenu.addSeparator(); + editMenu.add(selectAllSequenceMenuItem); + editMenu.add(deselectAllSequenceMenuItem); + editMenu.add(invertSequenceMenuItem); + editMenu.add(invertColSel); + editMenu.add(deleteGroups); + editMenu.addSeparator(); + editMenu.add(remove2LeftMenuItem); + editMenu.add(remove2RightMenuItem); + editMenu.add(removeGappedColumnMenuItem); + editMenu.add(removeAllGapsMenuItem); + editMenu.add(removeRedundancyMenuItem); + searchMenu.add(findMenuItem); + viewMenu.add(font); + viewMenu.addSeparator(); + viewMenu.add(menu1); + viewMenu.add(menu2); + viewMenu.addSeparator(); + viewMenu.add(wrapMenuItem); + viewMenu.add(scaleAbove); + viewMenu.add(scaleLeft); + viewMenu.add(scaleRight); + viewMenu.addSeparator(); + viewMenu.add(seqLimits); + viewMenu.add(viewBoxesMenuItem); + viewMenu.add(viewTextMenuItem); + viewMenu.add(colourTextMenuItem); + viewMenu.add(renderGapsMenuItem); + viewMenu.add(annotationPanelMenuItem); + viewMenu.addSeparator(); + viewMenu.add(sequenceFeatures); + viewMenu.add(featureSettings); + viewMenu.addSeparator(); + viewMenu.add(overviewMenuItem); + colourMenu.add(applyToAllGroups); + colourMenu.addSeparator(); + colourMenu.add(noColourmenuItem); + colourMenu.add(clustalColour); + colourMenu.add(BLOSUM62Colour); + colourMenu.add(PIDColour); + colourMenu.add(zappoColour); + colourMenu.add(taylorColour); + colourMenu.add(hydrophobicityColour); + colourMenu.add(helixColour); + colourMenu.add(strandColour); + colourMenu.add(turnColour); + colourMenu.add(buriedColour); + colourMenu.add(nucleotideColour); + colourMenu.add(userDefinedColour); + colourMenu.addSeparator(); + colourMenu.add(conservationMenuItem); + colourMenu.add(modifyConservation); + colourMenu.add(abovePIDThreshold); + colourMenu.add(modifyPID); + colourMenu.add(annotationColour); + calculateMenu.add(sort); + calculateMenu.add(calculate); + calculateMenu.addSeparator(); + calculateMenu.add(pairwiseAlignmentMenuItem); + calculateMenu.add(PCAMenuItem); + calculateMenu.add(autoCalculate); + this.add(statusBar, BorderLayout.SOUTH); + pasteMenu.add(pasteNew); + pasteMenu.add(pasteThis); + sort.add(sortIDMenuItem); + sort.add(sortByTreeMenu); + sort.add(sortGroupMenuItem); + sort.add(sortPairwiseMenuItem); + calculate.add(averageDistanceTreeMenuItem); + calculate.add(neighbourTreeMenuItem); + calculate.add(avDistanceTreeBlosumMenuItem); + calculate.add(njTreeBlosumMenuItem); + helpMenu.add(documentation); + helpMenu.add(about); + menu1.add(showColumns); + menu1.add(showSeqs); + menu2.add(hideColumns); + menu2.add(hideSequences); + } + + public void setEmbedded() + { + + embeddedMenu = new Panel(); + embeddedEdit = new Label(); + embeddedSearch = new Label(); + embeddedView = new Label(); + embeddedColour = new Label(); + embeddedFile = new Label(); + embeddedHelp = new Label(); + embeddedCalculate = new Label(); + flowLayout1 = new FlowLayout(); + embeddedMenu.setBackground(Color.lightGray); + embeddedMenu.setLayout(flowLayout1); + embeddedEdit.setText("Edit"); + embeddedEdit.setFont(new java.awt.Font("Arial", Font.PLAIN, 10)); + embeddedSearch.setText("Search"); + embeddedSearch.setFont(new java.awt.Font("Arial", Font.PLAIN, 10)); + embeddedView.setText("View"); + embeddedView.setFont(new java.awt.Font("Arial", Font.PLAIN, 10)); + embeddedColour.setText("Colour"); + embeddedColour.setFont(new java.awt.Font("Arial", Font.PLAIN, 10)); + embeddedFile.setFont(new java.awt.Font("Arial", Font.PLAIN, 10)); + embeddedFile.setText("File"); + embeddedHelp.setFont(new java.awt.Font("Arial", Font.PLAIN, 10)); + embeddedHelp.setText("Help"); + embeddedCalculate.setFont(new java.awt.Font("Arial", Font.PLAIN, 10)); + embeddedCalculate.setText("Calculate"); + embeddedMenu.add(embeddedFile); + embeddedMenu.add(embeddedEdit); + embeddedMenu.add(embeddedSearch); + embeddedMenu.add(embeddedView); + embeddedMenu.add(embeddedColour); + embeddedMenu.add(embeddedCalculate); + embeddedMenu.add(embeddedHelp); + flowLayout1.setAlignment(FlowLayout.LEFT); + flowLayout1.setHgap(2); + flowLayout1.setVgap(0); + embeddedFile.addMouseListener(this); + embeddedEdit.addMouseListener(this); + embeddedSearch.addMouseListener(this); + embeddedView.addMouseListener(this); + embeddedColour.addMouseListener(this); + embeddedCalculate.addMouseListener(this); + embeddedHelp.addMouseListener(this); + + // setVisible(false); + fileMenu.remove(closeMenuItem); + fileMenu.remove(3); // Seperator + + viewport.applet.setLayout(new BorderLayout()); + viewport.applet.add(embeddedMenu, BorderLayout.NORTH); + viewport.applet.add(statusBar, BorderLayout.SOUTH); + // viewport.applet.validate(); + + alignPanel.setSize(viewport.applet.size().width, viewport.applet.size().height + - embeddedMenu.HEIGHT - statusBar.HEIGHT); + + viewport.applet.add(alignPanel, BorderLayout.CENTER); + viewport.applet.validate(); + + } + + + + PopupMenu filePopup, editPopup, searchPopup, + viewPopup, colourPopup, calculatePopup, helpPopup; + MenuItem featureSettings = new MenuItem(); + CheckboxMenuItem sequenceFeatures = new CheckboxMenuItem(); + MenuItem annotationColour = new MenuItem(); + MenuItem invertColSel = new MenuItem(); + Menu menu1 = new Menu(); + MenuItem showColumns = new MenuItem(); + MenuItem showSeqs = new MenuItem(); + Menu menu2 = new Menu(); + MenuItem hideColumns = new MenuItem(); + MenuItem hideSequences = new MenuItem(); + + public void mousePressed(MouseEvent evt) + { + PopupMenu popup = null; + Label source = (Label)evt.getSource(); + if(source==embeddedFile) + { + popup = filePopup = genPopupMenu(filePopup, fileMenu); + } + else if(source==embeddedEdit) + { + popup = editPopup = genPopupMenu(editPopup, editMenu); + } + else if(source==embeddedSearch) + { + popup = searchPopup = genPopupMenu(searchPopup, searchMenu); + } + else if(source==embeddedView) + { + popup = viewPopup = genPopupMenu(viewPopup, viewMenu); + } + else if(source==embeddedColour) + { + popup = colourPopup = genPopupMenu(colourPopup, colourMenu); + } + else if(source==embeddedCalculate) + { + popup = calculatePopup = genPopupMenu(calculatePopup, calculateMenu); + } + else if(source==embeddedHelp) + { + popup = helpPopup = genPopupMenu(helpPopup, helpMenu); + } + + embeddedMenu.add(popup); + popup.show(embeddedMenu, + source.getBounds().x, + source.getBounds().y + source.getBounds().getSize().height); + } + + PopupMenu genPopupMenu(PopupMenu popup, Menu original) + { + if(popup!=null) + { + return popup; + } + popup = new PopupMenu(); + int m, mSize = original.getItemCount(); + for(m=0; m max) - { - max = columnAt(i); - } - } - - return max; - } - - /** - * DOCUMENT ME! - * - * @return DOCUMENT ME! - */ - public int getMin() - { - int min = 1000000000; - - for (int i = 0; i < selected.size(); i++) - { - if (columnAt(i) < min) - { - min = columnAt(i); - } - } - - return min; - } - - - /** - * propagate shift in alignment columns to column selection - * - * @param start beginning of edit - * @param change shift in edit (-ve or +ve number of columns) - */ - public void compensateForEdit(int start, int change) - { - for (int i = 0; i < size(); i++) - { - int temp = columnAt(i); - - if (temp >= start) - { - selected.setElementAt(new Integer(temp - change), i); - } - } - - if(hiddenColumns!=null) - { - for(int i=0; i start) - { - region[0] -= change; - region[1] -= change; - } - if(region[0]<0) - region[0] = 0; - if(region[1] <0) - region[1] = 0; - } - } - } - public ShiftList compensateForEdits(ShiftList shiftrecord) { - if (shiftrecord!=null) { - Vector shifts = shiftrecord.shifts; - if (shifts!=null && shifts.size()>0) { - for (int i=0,j=shifts.size(); i= region[0]) - { - result += region[1] - region[0] + 1; - } - } - } - return result; - } - - /** - * Use this method to find out where a visible column is in the alignment - * when hidden columns exist - * @param hiddenColumn int - * @return int - */ - public int findColumnPosition(int hiddenColumn) - { - int result = hiddenColumn; - if (hiddenColumns != null) - { - int index = 0; - int gaps = 0; - do - { - int[] region = (int[]) hiddenColumns.elementAt(index); - if (hiddenColumn > region[1]) - { - result -= region[1]+1-region[0]; - } - index++; - } - while (index < hiddenColumns.size()); - - result -= gaps; - } - - return result; - } - - /** - * Use this method to determine where the next hiddenRegion starts - */ - public int findHiddenRegionPosition(int hiddenRegion) - { - int result = 0; - if (hiddenColumns != null) - { - int index = 0; - int gaps = 0; - do - { - int[] region = (int[]) hiddenColumns.elementAt(index); - if(hiddenRegion==0) - { - return region[0]; - } - - gaps += region[1] +1 - region[0]; - result = region[1] +1; - index++; - } - while(index < hiddenRegion+1); - - result -= gaps; - } - - return result; - } - - /** - * THis method returns the rightmost limit of a - * region of an alignment with hidden columns. - * In otherwords, the next hidden column. - * @param index int - */ - public int getHiddenBoundaryRight(int alPos) - { - if (hiddenColumns != null) - { - int index = 0; - do - { - int[] region = (int[]) hiddenColumns.elementAt(index); - if(alPos < region[0]) - return region[0]; - - index++; - } - while(index < hiddenColumns.size()); - } - - return alPos; - - } - /** - * THis method returns the rightmost limit of a - * region of an alignment with hidden columns. - * In otherwords, the next hidden column. - * @param index int - */ - public int getHiddenBoundaryLeft(int alPos) - { - if (hiddenColumns != null) - { - int index = hiddenColumns.size()-1; - do - { - int[] region = (int[]) hiddenColumns.elementAt(index); - if(alPos > region[1]) - return region[1]; - - index--; - } - while(index >-1); - } - - return alPos; - - } - - public void hideSelectedColumns() - { - while (size() > 0) - { - int column = ( (Integer) getSelected().firstElement()).intValue(); - hideColumns(column); - } - - } - - public void hideColumns(int start, int end) - { - if(hiddenColumns==null) - hiddenColumns = new Vector(); - - boolean added = false; - boolean overlap = false; - - for (int i = 0; i < hiddenColumns.size(); i++) - { - int[] region = (int[]) hiddenColumns.elementAt(i); - if ( start<=region[1] && end>=region[0]) - { - hiddenColumns.removeElementAt(i); - overlap = true; - break; - } - else if (end < region[0] && start < region[0]) - { - hiddenColumns.insertElementAt(new int[] - {start, end}, i); - added = true; - break; - } - } - - if(overlap) - { - hideColumns(start, end); - } - else if (!added) - hiddenColumns.addElement(new int[] {start, end}); - - } - - /** - * This method will find a range of selected columns - * around the column specified - * @param res int - */ - public void hideColumns(int col) - { - // First find out range of columns to hide - int min = col, max = col+1; - while( contains(min) ) - { removeElement(min); min --; } - - while( contains(max) ) - { removeElement(max); max ++; } - - min++; max--; - - hideColumns(min, max); - } - - public void revealAllHiddenColumns() - { - if(hiddenColumns!=null) - { - for (int i = 0; i < hiddenColumns.size(); i++) - { - int[] region = (int[]) hiddenColumns.elementAt(i); - for (int j = region[0]; j < region[1]+1; j++) - { - addElement(j); - } - } - } - - hiddenColumns = null; - } - - public void revealHiddenColumns(int res) - { - for(int i=0; i= region[0] && column <= region[1]) - { - return false; - } - } - return true; - } - /** - * Copy constructor - * @param copy - */ - public ColumnSelection(ColumnSelection copy) { - if (copy!=null) { - if (copy.selected!=null) { - selected = new Vector(); - for (int i=0,j=copy.selected.size(); i max) + { + max = columnAt(i); + } + } + + return max; + } + + /** + * DOCUMENT ME! + * + * @return DOCUMENT ME! + */ + public int getMin() + { + int min = 1000000000; + + for (int i = 0; i < selected.size(); i++) + { + if (columnAt(i) < min) + { + min = columnAt(i); + } + } + + return min; + } + + + /** + * propagate shift in alignment columns to column selection + * + * @param start beginning of edit + * @param change shift in edit (-ve or +ve number of columns) + */ + public void compensateForEdit(int start, int change) + { + for (int i = 0; i < size(); i++) + { + int temp = columnAt(i); + + if (temp >= start) + { + selected.setElementAt(new Integer(temp - change), i); + } + } + + if(hiddenColumns!=null) + { + for(int i=0; i start) + { + region[0] -= change; + region[1] -= change; + } + if(region[0]<0) + region[0] = 0; + if(region[1] <0) + region[1] = 0; + } + } + } + public ShiftList compensateForEdits(ShiftList shiftrecord) { + if (shiftrecord!=null) { + Vector shifts = shiftrecord.shifts; + if (shifts!=null && shifts.size()>0) { + for (int i=0,j=shifts.size(); i= region[0]) + { + result += region[1] - region[0] + 1; + } + } + } + return result; + } + + /** + * Use this method to find out where a visible column is in the alignment + * when hidden columns exist + * @param hiddenColumn int + * @return int + */ + public int findColumnPosition(int hiddenColumn) + { + int result = hiddenColumn; + if (hiddenColumns != null) + { + int index = 0; + int gaps = 0; + do + { + int[] region = (int[]) hiddenColumns.elementAt(index); + if (hiddenColumn > region[1]) + { + result -= region[1]+1-region[0]; + } + index++; + } + while (index < hiddenColumns.size()); + + result -= gaps; + } + + return result; + } + + /** + * Use this method to determine where the next hiddenRegion starts + */ + public int findHiddenRegionPosition(int hiddenRegion) + { + int result = 0; + if (hiddenColumns != null) + { + int index = 0; + int gaps = 0; + do + { + int[] region = (int[]) hiddenColumns.elementAt(index); + if(hiddenRegion==0) + { + return region[0]; + } + + gaps += region[1] +1 - region[0]; + result = region[1] +1; + index++; + } + while(index < hiddenRegion+1); + + result -= gaps; + } + + return result; + } + + /** + * THis method returns the rightmost limit of a + * region of an alignment with hidden columns. + * In otherwords, the next hidden column. + * @param index int + */ + public int getHiddenBoundaryRight(int alPos) + { + if (hiddenColumns != null) + { + int index = 0; + do + { + int[] region = (int[]) hiddenColumns.elementAt(index); + if(alPos < region[0]) + return region[0]; + + index++; + } + while(index < hiddenColumns.size()); + } + + return alPos; + + } + /** + * THis method returns the rightmost limit of a + * region of an alignment with hidden columns. + * In otherwords, the next hidden column. + * @param index int + */ + public int getHiddenBoundaryLeft(int alPos) + { + if (hiddenColumns != null) + { + int index = hiddenColumns.size()-1; + do + { + int[] region = (int[]) hiddenColumns.elementAt(index); + if(alPos > region[1]) + return region[1]; + + index--; + } + while(index >-1); + } + + return alPos; + + } + + public void hideSelectedColumns() + { + while (size() > 0) + { + int column = ( (Integer) getSelected().firstElement()).intValue(); + hideColumns(column); + } + + } + + public void hideColumns(int start, int end) + { + if(hiddenColumns==null) + hiddenColumns = new Vector(); + + boolean added = false; + boolean overlap = false; + + for (int i = 0; i < hiddenColumns.size(); i++) + { + int[] region = (int[]) hiddenColumns.elementAt(i); + if ( start<=region[1] && end>=region[0]) + { + hiddenColumns.removeElementAt(i); + overlap = true; + break; + } + else if (end < region[0] && start < region[0]) + { + hiddenColumns.insertElementAt(new int[] + {start, end}, i); + added = true; + break; + } + } + + if(overlap) + { + hideColumns(start, end); + } + else if (!added) + hiddenColumns.addElement(new int[] {start, end}); + + } + + /** + * This method will find a range of selected columns + * around the column specified + * @param res int + */ + public void hideColumns(int col) + { + // First find out range of columns to hide + int min = col, max = col+1; + while( contains(min) ) + { removeElement(min); min --; } + + while( contains(max) ) + { removeElement(max); max ++; } + + min++; max--; + + hideColumns(min, max); + } + + public void revealAllHiddenColumns() + { + if(hiddenColumns!=null) + { + for (int i = 0; i < hiddenColumns.size(); i++) + { + int[] region = (int[]) hiddenColumns.elementAt(i); + for (int j = region[0]; j < region[1]+1; j++) + { + addElement(j); + } + } + } + + hiddenColumns = null; + } + + public void revealHiddenColumns(int res) + { + for(int i=0; i= region[0] && column <= region[1]) + { + return false; + } + } + return true; + } + /** + * Copy constructor + * @param copy + */ + public ColumnSelection(ColumnSelection copy) { + if (copy!=null) { + if (copy.selected!=null) { + selected = new Vector(); + for (int i=0,j=copy.selected.size(); iTitle: ShiftList

- * - *

Description:

- * - *

Copyright: Copyright (c) 2004

- * - *

Company: Dundee University

- * - * @author not attributable - * @version 1.0 - */ -public class ShiftList -{ - public Vector shifts; - public ShiftList() - { - shifts = new Vector(); - } - - /** - * addShift - * @param pos start position for shift (in original reference frame) - * @param shift length of shift - */ - public void addShift(int pos, int shift) - { - int sidx = 0; - int[] rshift=null; - while (sidx0) { - shiftList=new ShiftList(); - - for (int i=0,p=0; iTitle: ShiftList

+ * + *

Description:

+ * + *

Copyright: Copyright (c) 2004

+ * + *

Company: Dundee University

+ * + * @author not attributable + * @version 1.0 + */ +public class ShiftList +{ + public Vector shifts; + public ShiftList() + { + shifts = new Vector(); + } + + /** + * addShift + * @param pos start position for shift (in original reference frame) + * @param shift length of shift + */ + public void addShift(int pos, int shift) + { + int sidx = 0; + int[] rshift=null; + while (sidx0) { + shiftList=new ShiftList(); + + for (int i=0,p=0; i