X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FAlignFrame.java;h=e17af3893d7eff39cd9be75d8741c165da771b9b;hb=5c57814f95e73a63e012479651b919fdc4099f53;hp=5641846ba556004303de88d96fd0e736775f0a94;hpb=8da7acff9214ddaf0e6d28e76219ab51bd38e62d;p=jalview.git diff --git a/src/jalview/appletgui/AlignFrame.java b/src/jalview/appletgui/AlignFrame.java index 5641846..e17af38 100755 --- a/src/jalview/appletgui/AlignFrame.java +++ b/src/jalview/appletgui/AlignFrame.java @@ -1,1272 +1,2890 @@ -/* - * 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.jbappletgui.GAlignFrame; -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; - -public class AlignFrame - extends GAlignFrame -{ - final AlignmentPanel alignPanel; - final AlignViewport viewport; - public static final int NEW_WINDOW_WIDTH = 700; - public static final int NEW_WINDOW_HEIGHT = 500; - jalview.bin.JalviewLite applet; - - - public AlignFrame(AlignmentI al, jalview.bin.JalviewLite applet) - { - this.applet = applet; - viewport = new AlignViewport(al, applet); - alignPanel = new AlignmentPanel(this, viewport); - add(alignPanel); - alignPanel.validate(); - - String treeFile = applet.getParameter("treeFile"); - if (treeFile != null) - { - try - { - treeFile = treeFile; - jalview.io.NewickFile fin = new jalview.io.NewickFile(applet. - getCodeBase() + treeFile, "URL"); - fin.parse(); - - if (fin.getTree() != null) - { - TreePanel tp = null; - tp = new TreePanel(viewport, viewport.getAlignment().getSequences(), - fin, "FromFile", applet.getCodeBase() + treeFile); - jalview.bin.JalviewLite.addFrame(tp, treeFile, 600, 500); - addTreeMenuItem(tp, treeFile); - } - } - catch (Exception ex) - { - ex.printStackTrace(); - } - } - - String param = applet.getParameter("sortBy"); - if(param!=null) - { - if (param.equalsIgnoreCase("Id")) - sortIDMenuItem_actionPerformed(null); - else if (param.equalsIgnoreCase("Pairwise Identity")) - sortPairwiseMenuItem_actionPerformed(null); - } - - this.addWindowListener(new WindowAdapter() - { - public void windowClosing(WindowEvent e) - { - closeMenuItem_actionPerformed(null); - } - }); - - viewport.addPropertyChangeListener(new java.beans.PropertyChangeListener() - { - public void propertyChange(java.beans.PropertyChangeEvent evt) - { - if (evt.getPropertyName().equals("alignment")) - { - alignmentChanged(); - } - } - }); - } - - public void inputText_actionPerformed(ActionEvent e) - { - CutAndPasteTransfer cap = new CutAndPasteTransfer(true, applet); - 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, applet); - Frame frame = new Frame(); - frame.add(cap); - jalview.bin.JalviewLite.addFrame(frame, - "Alignment output - " + e.getActionCommand(), - 600, 500); - cap.setText(FormatAdapter.formatSequences(e.getActionCommand(), - viewport.getAlignment(). - getSequences())); - } - - public void closeMenuItem_actionPerformed(ActionEvent e) - { - PaintRefresher.components.remove(viewport.alignment); - 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); - updateEditMenuBar(); - } - - protected void undoMenuItem_actionPerformed(ActionEvent e) - { - HistoryItem hi = (HistoryItem) historyList.pop(); - redoList.push(new HistoryItem(hi.getDescription(), viewport.alignment, - HistoryItem.HIDE)); - restoreHistoryItem(hi); - viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences()); - } - - protected void redoMenuItem_actionPerformed(ActionEvent e) - { - HistoryItem hi = (HistoryItem) redoList.pop(); - restoreHistoryItem(hi); - updateEditMenuBar(); - viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences()); - } - - // used by undo and redo - void restoreHistoryItem(HistoryItem hi) - { - if (hi.getType() == HistoryItem.SORT) - { - for (int i = 0; i < hi.getSequences().size(); i++) - { - viewport.alignment.getSequences().setElementAt(hi.getSequences(). - elementAt(i), i); - } - } - else - { - for (int i = 0; i < hi.getSequences().size(); i++) - { - SequenceI restore = (SequenceI) hi.getSequences().elementAt(i); - if (restore.getLength() == 0) - { - // log.System.out.println(hi.getHidden().elementAt(i)); - restore.setSequence(hi.getHidden().elementAt(i).toString()); - viewport.alignment.getSequences().insertElementAt( - restore, - hi.getAlignIndex(i)); - } - else - { - restore.setSequence(hi.getHidden().elementAt(i).toString()); - } - } - if (hi.getType() == HistoryItem.PASTE) - { - for (int i = viewport.alignment.getHeight() - 1; - i > hi.getSequences().size() - 1; i--) - { - viewport.alignment.deleteSequence(i); - } - } - } - - 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.sequences.contains(seq)) - { - continue; - } - - SequenceI temp = viewport.alignment.getSequenceAt(i - 1); - if (sg.sequences.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.sequences.contains(seq)) - { - continue; - } - - SequenceI temp = viewport.alignment.getSequenceAt(i + 1); - if (sg.sequences.contains(temp)) - { - continue; - } - - viewport.alignment.getSequences().setElementAt(temp, i); - viewport.alignment.getSequences().setElementAt(seq, i + 1); - } - } - - alignPanel.repaint(); - } - - StringBuffer copiedSequences; - protected void copy_actionPerformed(ActionEvent e) - { - if (viewport.getSelectionGroup() == null) - { - return; - } - - SequenceGroup sg = viewport.getSelectionGroup(); - copiedSequences = new StringBuffer(); - Hashtable orderedSeqs = new Hashtable(); - for (int i = 0; i < sg.getSize(); i++) - { - SequenceI seq = sg.getSequenceAt(i); - int index = viewport.alignment.findIndex(seq); - orderedSeqs.put(index + "", seq); - } - - int index = 0, startRes, endRes; - char ch; - - for (int i = 0; i < sg.getSize(); i++) - { - SequenceI seq = null; - - while (seq == null) - { - if (orderedSeqs.containsKey(index + "")) - { - seq = (SequenceI) orderedSeqs.get(index + ""); - index++; - - break; - } - else - { - index++; - } - } - - //FIND START RES - //Returns residue following index if gap - startRes = seq.findPosition(sg.getStartRes()); - - //FIND END RES - //Need to find the residue preceeding index if gap - endRes = 0; - - for (int j = 0; j < sg.getEndRes()+1 && j < seq.getLength(); j++) - { - ch = seq.getCharAt(j); - if (!jalview.util.Comparison.isGap( (ch))) - { - endRes++; - } - } - - if(endRes>0) - { - endRes += seq.getStart() -1; - } - - copiedSequences.append(seq.getName() + "\t" + - startRes + "\t" + - endRes + "\t" + - seq.getSequence(sg.getStartRes(), - sg.getEndRes() + 1) + "\n"); - } - - } - - protected void pasteNew_actionPerformed(ActionEvent e) - { - paste(true); - } - - protected void pasteThis_actionPerformed(ActionEvent e) - { - 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); - } - - AlignFrame af = new AlignFrame(new Alignment(newSeqs), applet); - String newtitle = new String("Copied sequences"); - if (getTitle().startsWith("Copied sequences")) - { - newtitle = getTitle(); - } - else - { - newtitle = newtitle.concat("- from " + getTitle()); - } - 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(ActionEvent e) - { - copy_actionPerformed(null); - delete_actionPerformed(null); - } - - protected void delete_actionPerformed(ActionEvent e) - { - addHistoryItem(new HistoryItem("Delete Sequences", viewport.alignment, - HistoryItem.HIDE)); - if (viewport.getSelectionGroup() == null) - { - return; - } - - - SequenceGroup sg = viewport.getSelectionGroup(); - boolean allSequences = false; - if(sg.sequences.size()==viewport.alignment.getHeight()) - allSequences = true; - - for (int i = 0; i < sg.sequences.size(); 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(ActionEvent e) - { - viewport.alignment.deleteAllGroups(); - viewport.setSelectionGroup(null); - - alignPanel.repaint(); - } - - public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e) - { - 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(ActionEvent e) - { - viewport.setSelectionGroup(null); - viewport.getColumnSelection().clear(); - viewport.setSelectionGroup(null); - alignPanel.repaint(); - PaintRefresher.Refresh(null, viewport.alignment); - } - - public void invertSequenceMenuItem_actionPerformed(ActionEvent e) - { - 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(ActionEvent e) - { - ColumnSelection colSel = viewport.getColumnSelection(); - if (colSel.size() > 0) - { - addHistoryItem(new HistoryItem("Remove Left", viewport.alignment, - HistoryItem.HIDE)); - int min = colSel.getMin(); - viewport.getAlignment().trimLeft(min); - colSel.compensateForEdit(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(ActionEvent e) - { - 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(ActionEvent e) - { - addHistoryItem(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(ActionEvent e) - { - addHistoryItem(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; - int jSize; - - Vector seqs=null; - - int start=0, end = viewport.alignment.getWidth(); - - if (viewport.getSelectionGroup() != null - && viewport.getSelectionGroup().sequences != null - && viewport.getSelectionGroup().sequences.size()>0) - { - seqs = viewport.getSelectionGroup().sequences; - start = viewport.getSelectionGroup().getStartRes(); - end = viewport.getSelectionGroup().getEndRes(); - } - else - seqs = viewport.alignment.getSequences(); - - for (int i = 0; i 1) - { - Frame frame = new Frame(); - frame.add(new PairwiseAlignPanel(alignPanel)); - jalview.bin.JalviewLite.addFrame(frame, "Pairwise Alignment", 600, 500); - } - } - - public void PCAMenuItem_actionPerformed(ActionEvent e) - { - - if ( (viewport.getSelectionGroup() != null && - viewport.getSelectionGroup().getSize() < 4 && - viewport.getSelectionGroup().getSize() > 0) - || viewport.getAlignment().getHeight() < 4) - { - return; - } - - try - { - PCAPanel pcaPanel = new PCAPanel(viewport, null); - Frame frame = new Frame(); - frame.add(pcaPanel); - jalview.bin.JalviewLite.addFrame(frame, "Principal component analysis", - 400, 400); - } - catch (java.lang.OutOfMemoryError ex) - { - } - - } - - public void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e) - { - NewTreePanel("AV", "PID", "Average distance tree using PID"); - } - - public void neighbourTreeMenuItem_actionPerformed(ActionEvent e) - { - NewTreePanel("NJ", "PID", "Neighbour joining tree using PID"); - } - - protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e) - { - NewTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62"); - } - - protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e) - { - 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(); - - } - - final TreePanel tp; - if (viewport.getSelectionGroup() != null && - viewport.getSelectionGroup().getSize() > 3) - { - tp = new TreePanel(viewport, viewport.getSelectionGroup().sequences, type, - pwType, - 0, viewport.alignment.getWidth()); - } - else - { - tp = new TreePanel(viewport, viewport.getAlignment().getSequences(), - type, pwType, 0, viewport.alignment.getWidth()); - } - - addTreeMenuItem(tp, title); - - jalview.bin.JalviewLite.addFrame(tp, title, 600, 500); - } - - 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 e) - { - 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(ActionEvent e) - { - jalview.bin.JalviewLite.showURL("http://www.jalview.org/help.html"); - } - - protected void about_actionPerformed(ActionEvent e) - { - - 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 12;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); - - } -} +/* + * Jalview - A Sequence Alignment Editor and Viewer + * Copyright (C) 2007 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 java.io.*; +import java.net.*; +import java.util.*; + +import java.awt.*; +import java.awt.event.*; + +import jalview.analysis.*; +import jalview.commands.*; +import jalview.datamodel.*; +import jalview.io.*; +import jalview.schemes.*; + +public class AlignFrame + extends Frame implements ActionListener, + ItemListener, KeyListener, MouseListener +{ + public AlignmentPanel alignPanel; + public AlignViewport viewport; + int DEFAULT_WIDTH = 700; + int DEFAULT_HEIGHT = 500; + + String jalviewServletURL; + + public AlignFrame(AlignmentI al, + jalview.bin.JalviewLite applet, + String title, + boolean embedded) + { + + if (applet != null) + { + jalviewServletURL = applet.getParameter("APPLICATION_URL"); + } + + try + { + jbInit(); + } + catch (Exception ex) + { + ex.printStackTrace(); + } + + viewport = new AlignViewport(al, applet); + alignPanel = new AlignmentPanel(this, viewport); + + viewport.updateConservation(alignPanel); + viewport.updateConsensus(alignPanel); + + annotationPanelMenuItem.setState(viewport.showAnnotation); + + 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); + DEFAULT_WIDTH = width; + } + param = applet.getParameter("windowHeight"); + if (param != null) + { + int height = Integer.parseInt(param); + DEFAULT_HEIGHT = height; + } + } + catch (Exception ex) + {} + + } + + //Some JVMS send keyevents to Top frame or lowest panel, + //Havent worked out why yet. So add to both this frame and seqCanvas for now + this.addKeyListener(this); + alignPanel.seqPanel.seqCanvas.addKeyListener(this); + alignPanel.idPanel.idCanvas.addKeyListener(this); + alignPanel.scalePanel.addKeyListener(this); + alignPanel.annotationPanel.addKeyListener(this); + + if (embedded) + { + setEmbedded(); + } + else + { + add(alignPanel, BorderLayout.CENTER); + jalview.bin.JalviewLite.addFrame(this, title, DEFAULT_WIDTH, + DEFAULT_HEIGHT); + } + alignPanel.validate(); + alignPanel.paintAlignment(true); + } + + public AlignViewport getAlignViewport() + { + return viewport; + } + + public SeqCanvas getSeqcanvas() + { + return alignPanel.seqPanel.seqCanvas; + } + + /** + * DOCUMENT ME! + * + * @param String DOCUMENT ME! + */ + + public void parseFeaturesFile(String file, String type) + { + Hashtable featureLinks = new Hashtable(); + boolean featuresFile = false; + try + { + featuresFile = new jalview.io.FeaturesFile(file, + type).parse(viewport.alignment, + alignPanel.seqPanel.seqCanvas. + getFeatureRenderer().featureColours, + featureLinks, + true); + } + catch (Exception ex) + { + ex.printStackTrace(); + } + + if (featuresFile) + { + if (featureLinks.size() > 0) + { + alignPanel.seqPanel.seqCanvas + .getFeatureRenderer().featureLinks = featureLinks; + } + viewport.showSequenceFeatures = true; + sequenceFeatures.setState(true); + alignPanel.paintAlignment(true); + } + + } + + public void keyPressed(KeyEvent evt) + { + if (viewport.cursorMode && + ( (evt.getKeyCode() >= KeyEvent.VK_0 && + evt.getKeyCode() <= KeyEvent.VK_9) + || + (evt.getKeyCode() >= KeyEvent.VK_NUMPAD0 && + evt.getKeyCode() <= KeyEvent.VK_NUMPAD9) + ) + && Character.isDigit(evt.getKeyChar())) + alignPanel.seqPanel.numberPressed(evt.getKeyChar()); + + + switch (evt.getKeyCode()) + { + case 27: // escape key + deselectAllSequenceMenuItem_actionPerformed(); + break; + case KeyEvent.VK_X: + if (evt.isControlDown() || evt.isMetaDown()) + { + cut_actionPerformed(); + } + break; + case KeyEvent.VK_C: + if (viewport.cursorMode && !evt.isControlDown()) + { + alignPanel.seqPanel.setCursorColumn(); + } + if (evt.isControlDown() || evt.isMetaDown()) + { + copy_actionPerformed(); + } + break; + case KeyEvent.VK_V: + if (evt.isControlDown()) + { + paste(evt.isShiftDown()); + } + break; + case KeyEvent.VK_A: + if (evt.isControlDown() || evt.isMetaDown()) + { + selectAllSequenceMenuItem_actionPerformed(); + } + break; + case KeyEvent.VK_DOWN: + if (viewport.cursorMode) + { + alignPanel.seqPanel.moveCursor(0, 1); + } + else + { + moveSelectedSequences(false); + } + break; + + case KeyEvent.VK_UP: + if (viewport.cursorMode) + { + alignPanel.seqPanel.moveCursor(0, -1); + } + else + { + moveSelectedSequences(true); + } + break; + + case KeyEvent.VK_LEFT: + if (evt.isAltDown() || !viewport.cursorMode) + slideSequences(false, + alignPanel.seqPanel.getKeyboardNo1()); + else + alignPanel.seqPanel.moveCursor( -1, 0); + break; + + case KeyEvent.VK_RIGHT: + if (evt.isAltDown() || !viewport.cursorMode) + slideSequences(true, + alignPanel.seqPanel.getKeyboardNo1()); + else + alignPanel.seqPanel.moveCursor( 1, 0); + break; + + case KeyEvent.VK_SPACE: + if (viewport.cursorMode) + { + alignPanel.seqPanel.insertGapAtCursor(evt.isControlDown() + || evt.isShiftDown() + || evt.isAltDown() + ); + } + break; + + case KeyEvent.VK_DELETE: + case KeyEvent.VK_BACK_SPACE: + if (viewport.cursorMode) + { + alignPanel.seqPanel.deleteGapAtCursor(evt.isControlDown() + || evt.isShiftDown() + || evt.isAltDown()); + } + else + { + cut_actionPerformed(); + alignPanel.seqPanel.seqCanvas.repaint(); + } + break; + + case KeyEvent.VK_S: + if (viewport.cursorMode) + { + alignPanel.seqPanel.setCursorRow(); + } + break; + case KeyEvent.VK_P: + if (viewport.cursorMode) + { + alignPanel.seqPanel.setCursorPosition(); + } + break; + + case KeyEvent.VK_ENTER: + case KeyEvent.VK_COMMA: + if (viewport.cursorMode) + { + alignPanel.seqPanel.setCursorRowAndColumn(); + } + break; + + case KeyEvent.VK_Q: + if (viewport.cursorMode) + { + alignPanel.seqPanel.setSelectionAreaAtCursor(true); + } + break; + case KeyEvent.VK_M: + if (viewport.cursorMode) + { + alignPanel.seqPanel.setSelectionAreaAtCursor(false); + } + break; + + case KeyEvent.VK_F2: + viewport.cursorMode = !viewport.cursorMode; + statusBar.setText("Keyboard editing mode is " + + (viewport.cursorMode ? "on" : "off")); + if (viewport.cursorMode) + { + alignPanel.seqPanel.seqCanvas.cursorX = viewport.startRes; + alignPanel.seqPanel.seqCanvas.cursorY = viewport.startSeq; + } + break; + + case KeyEvent.VK_F: + if (evt.isControlDown()) + { + findMenuItem_actionPerformed(); + } + break; + + case KeyEvent.VK_H: + { + boolean toggleSeqs = !evt.isControlDown(); + boolean toggleCols = !evt.isShiftDown(); + boolean hide = false; + SequenceGroup sg = viewport.getSelectionGroup(); + + if (toggleSeqs) + { + if (sg != null && sg.getSize() != viewport.alignment.getHeight()) + { + hide = true; + viewport.hideAllSelectedSeqs(); + } + else if (! (toggleCols && viewport.colSel.getSelected().size() > 0)) + { + viewport.showAllHiddenSeqs(); + } + } + + if (toggleCols) + { + if (viewport.colSel.getSelected().size() > 0) + { + viewport.hideSelectedColumns(); + if (!toggleSeqs) + { + viewport.selectionGroup = sg; + } + } + else if (!hide) + { + viewport.showAllHiddenColumns(); + } + } + break; + } + + case KeyEvent.VK_PAGE_UP: + if (viewport.wrapAlignment) + { + alignPanel.scrollUp(true); + } + else + { + alignPanel.setScrollValues(viewport.startRes, + viewport.startSeq + - viewport.endSeq + viewport.startSeq); + } + break; + + case KeyEvent.VK_PAGE_DOWN: + if (viewport.wrapAlignment) + { + alignPanel.scrollUp(false); + } + else + { + alignPanel.setScrollValues(viewport.startRes, + viewport.startSeq + + viewport.endSeq - viewport.startSeq); + } + break; + + case KeyEvent.VK_Z: + if (evt.isControlDown()) + { + undoMenuItem_actionPerformed(); + } + break; + + case KeyEvent.VK_Y: + if (evt.isControlDown()) + { + redoMenuItem_actionPerformed(); + } + break; + + case KeyEvent.VK_L: + if (evt.isControlDown()) + { + trimAlignment(true); + } + break; + + case KeyEvent.VK_R: + if (evt.isControlDown()) + { + trimAlignment(false); + } + break; + + case KeyEvent.VK_E: + if (evt.isControlDown()) + { + if (evt.isShiftDown()) + { + this.removeAllGapsMenuItem_actionPerformed(); + } + else + { + removeGappedColumnMenuItem_actionPerformed(); + } + } + break; + case KeyEvent.VK_I: + if (evt.isControlDown()) + { + if (evt.isAltDown()) + { + viewport.invertColumnSelection(); + } + else + { + this.invertSequenceMenuItem_actionPerformed(); + } + } + break; + + case KeyEvent.VK_U: + if (evt.isControlDown()) + { + this.deleteGroups_actionPerformed(); + } + break; + + case KeyEvent.VK_T: + if (evt.isControlDown()) + { + newView(); + } + break; + + } + alignPanel.paintAlignment(true); + } + + 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) + { + viewport.setScaleAboveWrapped(scaleAbove.getState()); + } + else if (evt.getSource() == scaleLeft) + { + viewport.setScaleLeftWrapped(scaleLeft.getState()); + } + else if (evt.getSource() == scaleRight) + { + viewport.setScaleRightWrapped(scaleRight.getState()); + } + else if (evt.getSource() == seqLimits) + { + seqLimits_itemStateChanged(); + } + else if (evt.getSource() == viewBoxesMenuItem) + { + viewport.setShowBoxes(viewBoxesMenuItem.getState()); + } + else if (evt.getSource() == viewTextMenuItem) + { + viewport.setShowText(viewTextMenuItem.getState()); + } + else if (evt.getSource() == renderGapsMenuItem) + { + viewport.setRenderGaps(renderGapsMenuItem.getState()); + } + else if (evt.getSource() == annotationPanelMenuItem) + { + viewport.setShowAnnotation(annotationPanelMenuItem.getState()); + alignPanel.setAnnotationVisible(annotationPanelMenuItem.getState()); + } + else if (evt.getSource() == sequenceFeatures) + { + viewport.showSequenceFeatures(sequenceFeatures.getState()); + alignPanel.seqPanel.seqCanvas.repaint(); + } + else if (evt.getSource() == conservationMenuItem) + { + conservationMenuItem_actionPerformed(); + } + else if (evt.getSource() == abovePIDThreshold) + { + abovePIDThreshold_actionPerformed(); + } + else if (evt.getSource() == applyToAllGroups) + { + viewport.setColourAppliesToAllGroups(applyToAllGroups.getState()); + } + else if (evt.getSource() == autoCalculate) + { + viewport.autocalculateConsensus = autoCalculate.getState(); + } + + alignPanel.paintAlignment(true); + } + + public void actionPerformed(ActionEvent evt) + { + Object source = evt.getSource(); + + if (source == inputText) + { + inputText_actionPerformed(); + } + else if (source == loadTree) + { + loadTree_actionPerformed(); + } + else if (source == loadApplication) + { + launchFullApplication(); + } + else if (source == loadAnnotations) + { + loadAnnotations(); + } + else if (source == outputAnnotations) + { + outputAnnotations(true); + } + else if (source == outputFeatures) + { + outputFeatures(true, "Jalview"); + } + else if (source == closeMenuItem) + { + closeMenuItem_actionPerformed(); + } + else if (source == copy) + { + copy_actionPerformed(); + } + else if (source == undoMenuItem) + { + undoMenuItem_actionPerformed(); + } + else if (source == redoMenuItem) + { + redoMenuItem_actionPerformed(); + } + else if (source == inputText) + { + inputText_actionPerformed(); + } + else if (source == closeMenuItem) + { + closeMenuItem_actionPerformed(); + } + else if (source == undoMenuItem) + { + undoMenuItem_actionPerformed(); + } + else if (source == redoMenuItem) + { + redoMenuItem_actionPerformed(); + } + else if (source == copy) + { + copy_actionPerformed(); + } + else if (source == pasteNew) + { + pasteNew_actionPerformed(); + } + else if (source == pasteThis) + { + pasteThis_actionPerformed(); + } + else if (source == cut) + { + cut_actionPerformed(); + } + else if (source == delete) + { + delete_actionPerformed(); + } + else if (source == deleteGroups) + { + deleteGroups_actionPerformed(); + } + else if (source == selectAllSequenceMenuItem) + { + selectAllSequenceMenuItem_actionPerformed(); + } + else if (source == deselectAllSequenceMenuItem) + { + deselectAllSequenceMenuItem_actionPerformed(); + } + else if (source == invertSequenceMenuItem) + { + invertSequenceMenuItem_actionPerformed(); + } + else if (source == invertColSel) + { + viewport.invertColumnSelection(); + alignPanel.paintAlignment(true); + } + else if (source == remove2LeftMenuItem) + { + trimAlignment(true); + } + else if (source == remove2RightMenuItem) + { + trimAlignment(false); + } + else if (source == removeGappedColumnMenuItem) + { + removeGappedColumnMenuItem_actionPerformed(); + } + else if (source == removeAllGapsMenuItem) + { + removeAllGapsMenuItem_actionPerformed(); + } + else if (source == findMenuItem) + { + findMenuItem_actionPerformed(); + } + else if (source == font) + { + new FontChooser(alignPanel); + } + else if (source == newView) + { + newView(); + } + else if (source == showColumns) + { + viewport.showAllHiddenColumns(); + alignPanel.paintAlignment(true); + } + else if (source == showSeqs) + { + viewport.showAllHiddenSeqs(); + } + else if (source == hideColumns) + { + viewport.hideSelectedColumns(); + alignPanel.paintAlignment(true); + } + else if (source == hideSequences && viewport.getSelectionGroup() != null) + { + viewport.hideAllSelectedSeqs(); + } + else if (source == featureSettings) + { + new FeatureSettings(alignPanel); + } + else if(source== alProperties) + { + StringBuffer contents = new StringBuffer(); + + float avg = 0; + int min=Integer.MAX_VALUE, max=0; + for(int i=0; imax) + max = size; + if(size 0) + { + undoMenuItem.setEnabled(true); + CommandI command = (CommandI) viewport.historyList.peek(); + undoMenuItem.setLabel("Undo " + command.getDescription()); + } + else + { + undoMenuItem.setEnabled(false); + undoMenuItem.setLabel("Undo"); + } + + if (viewport.redoList.size() > 0) + { + redoMenuItem.setEnabled(true); + + CommandI command = (CommandI) viewport.redoList.peek(); + redoMenuItem.setLabel("Redo " + command.getDescription()); + } + else + { + redoMenuItem.setEnabled(false); + redoMenuItem.setLabel("Redo"); + } + } + + public void addHistoryItem(CommandI command) + { + if (command.getSize() > 0) + { + viewport.historyList.push(command); + viewport.redoList.removeAllElements(); + updateEditMenuBar(); + viewport.hasHiddenColumns = viewport.colSel.getHiddenColumns() != null; + } + } + /** + * DOCUMENT ME! + * + * @param e DOCUMENT ME! + */ + protected void undoMenuItem_actionPerformed() + { + if (viewport.historyList.size() < 1) + { + return; + } + + CommandI command = (CommandI) viewport.historyList.pop(); + viewport.redoList.push(command); + command.undoCommand(null); + + AlignViewport originalSource = getOriginatingSource(command); + + originalSource.hasHiddenColumns = viewport.colSel.getHiddenColumns() != null; + updateEditMenuBar(); + originalSource.firePropertyChange("alignment", null, + originalSource.alignment.getSequences()); + } + + /** + * DOCUMENT ME! + * + * @param e DOCUMENT ME! + */ + protected void redoMenuItem_actionPerformed() + { + if (viewport.redoList.size() < 1) + { + return; + } + + CommandI command = (CommandI) viewport.redoList.pop(); + viewport.historyList.push(command); + command.doCommand(null); + + AlignViewport originalSource = getOriginatingSource(command); + originalSource.hasHiddenColumns = viewport.colSel.getHiddenColumns() != null; + + updateEditMenuBar(); + originalSource.firePropertyChange("alignment", null, + originalSource.alignment.getSequences()); + } + + AlignViewport getOriginatingSource(CommandI command) + { + AlignViewport originalSource = null; + //For sequence removal and addition, we need to fire + //the property change event FROM the viewport where the + //original alignment was altered + AlignmentI al = null; + if (command instanceof EditCommand) + { + EditCommand editCommand = (EditCommand) command; + al = editCommand.getAlignment(); + Vector comps = (Vector) PaintRefresher.components + .get(viewport.getSequenceSetId()); + for (int i = 0; i < comps.size(); i++) + { + if (comps.elementAt(i) instanceof AlignmentPanel) + { + if (al == ( (AlignmentPanel) comps.elementAt(i)).av.alignment) + { + originalSource = ( (AlignmentPanel) comps.elementAt(i)).av; + break; + } + } + } + } + + if (originalSource == null) + { + //The original view is closed, we must validate + //the current view against the closed view first + if (al != null) + { + PaintRefresher.validateSequences(al, viewport.alignment); + } + + originalSource = viewport; + } + + return originalSource; + } + + public void moveSelectedSequences(boolean up) + { + SequenceGroup sg = viewport.getSelectionGroup(); + if (sg == null) + { + return; + } + + if (up) + { + for (int i = 1; i < viewport.alignment.getHeight(); i++) + { + SequenceI seq = viewport.alignment.getSequenceAt(i); + if (!sg.getSequences(null).contains(seq)) + { + continue; + } + + SequenceI temp = viewport.alignment.getSequenceAt(i - 1); + if (sg.getSequences(null).contains(temp)) + { + continue; + } + + viewport.alignment.getSequences().setElementAt(temp, i); + viewport.alignment.getSequences().setElementAt(seq, i - 1); + } + } + else + { + for (int i = viewport.alignment.getHeight() - 2; i > -1; i--) + { + SequenceI seq = viewport.alignment.getSequenceAt(i); + if (!sg.getSequences(viewport.hiddenRepSequences).contains(seq)) + { + continue; + } + + SequenceI temp = viewport.alignment.getSequenceAt(i + 1); + if (sg.getSequences(viewport.hiddenRepSequences).contains(temp)) + { + continue; + } + + viewport.alignment.getSequences().setElementAt(temp, i); + viewport.alignment.getSequences().setElementAt(seq, i + 1); + } + } + + alignPanel.paintAlignment(true); + } + + synchronized void slideSequences(boolean right, int size) + { + Vector sg = new Vector(); + if(viewport.cursorMode) + { + sg.addElement(viewport.alignment.getSequenceAt( + alignPanel.seqPanel.seqCanvas.cursorY)); + } + else if(viewport.getSelectionGroup()!=null + && viewport.getSelectionGroup().getSize()!=viewport.alignment.getHeight()) + { + sg = viewport.getSelectionGroup().getSequences( + viewport.hiddenRepSequences); + } + + if(sg.size()<1) + { + return; + } + + Vector invertGroup = new Vector(); + + for (int i = 0; i < viewport.alignment.getHeight(); i++) + { + if(!sg.contains(viewport.alignment.getSequenceAt(i))) + invertGroup.addElement(viewport.alignment.getSequenceAt(i)); + } + + SequenceI[] seqs1 = new SequenceI[sg.size()]; + for (int i = 0; i < sg.size(); i++) + seqs1[i] = (SequenceI) sg.elementAt(i); + + SequenceI[] seqs2 = new SequenceI[invertGroup.size()]; + for (int i = 0; i < invertGroup.size(); i++) + seqs2[i] = (SequenceI) invertGroup.elementAt(i); + + SlideSequencesCommand ssc; + if (right) + ssc = new SlideSequencesCommand("Slide Sequences", + seqs2, seqs1, size, + viewport.getGapCharacter() + ); + else + ssc = new SlideSequencesCommand("Slide Sequences", + seqs1, seqs2, size, + viewport.getGapCharacter() + ); + + int groupAdjustment = 0; + if (ssc.getGapsInsertedBegin() && right) + { + if (viewport.cursorMode) + alignPanel.seqPanel.moveCursor(size, 0); + else + groupAdjustment = size; + } + else if (!ssc.getGapsInsertedBegin() && !right) + { + if (viewport.cursorMode) + alignPanel.seqPanel.moveCursor( -size, 0); + else + groupAdjustment = -size; + } + + if (groupAdjustment != 0) + { + viewport.getSelectionGroup().setStartRes( + viewport.getSelectionGroup().getStartRes() + groupAdjustment); + viewport.getSelectionGroup().setEndRes( + viewport.getSelectionGroup().getEndRes() + groupAdjustment); + } + + + boolean appendHistoryItem = false; + if(viewport.historyList!=null + && viewport.historyList.size()>0 + && viewport.historyList.peek() instanceof SlideSequencesCommand) + { + appendHistoryItem = ssc.appendSlideCommand( + (SlideSequencesCommand)viewport.historyList.peek()) + ; + } + + if(!appendHistoryItem) + addHistoryItem(ssc); + + repaint(); + } + + static StringBuffer copiedSequences; + static Vector copiedHiddenColumns; + protected void copy_actionPerformed() + { + if (viewport.getSelectionGroup() == null) + { + return; + } + + SequenceGroup sg = viewport.getSelectionGroup(); + copiedSequences = new StringBuffer(); + Hashtable orderedSeqs = new Hashtable(); + for (int i = 0; i < sg.getSize(); i++) + { + SequenceI seq = sg.getSequenceAt(i); + int index = viewport.alignment.findIndex(seq); + orderedSeqs.put(index + "", seq); + } + + int index = 0, startRes, endRes; + char ch; + + if (viewport.hasHiddenColumns && viewport.getSelectionGroup() != null) + { + copiedHiddenColumns = new Vector(); + int hiddenOffset = viewport.getSelectionGroup().getStartRes(); + for (int i = 0; i < viewport.getColumnSelection().getHiddenColumns().size(); + i++) + { + int[] region = (int[]) + viewport.getColumnSelection().getHiddenColumns().elementAt(i); + + copiedHiddenColumns.addElement(new int[] + {region[0] - hiddenOffset, + region[1] - hiddenOffset}); + } + } + else + { + copiedHiddenColumns = null; + } + + for (int i = 0; i < sg.getSize(); i++) + { + SequenceI seq = null; + + while (seq == null) + { + if (orderedSeqs.containsKey(index + "")) + { + seq = (SequenceI) orderedSeqs.get(index + ""); + index++; + + break; + } + else + { + index++; + } + } + + //FIND START RES + //Returns residue following index if gap + startRes = seq.findPosition(sg.getStartRes()); + + //FIND END RES + //Need to find the residue preceeding index if gap + endRes = 0; + + for (int j = 0; j < sg.getEndRes() + 1 && j < seq.getLength(); j++) + { + ch = seq.getCharAt(j); + if (!jalview.util.Comparison.isGap( (ch))) + { + endRes++; + } + } + + if (endRes > 0) + { + endRes += seq.getStart() - 1; + } + + copiedSequences.append(seq.getName() + "\t" + + startRes + "\t" + + endRes + "\t" + + seq.getSequenceAsString(sg.getStartRes(), + sg.getEndRes() + 1) + "\n"); + } + + } + + protected void pasteNew_actionPerformed() + { + paste(true); + } + + protected void pasteThis_actionPerformed() + { + paste(false); + } + + void paste(boolean newAlignment) + { + try + { + + if (copiedSequences == null) + { + return; + } + + StringTokenizer st = new StringTokenizer(copiedSequences.toString()); + Vector seqs = new Vector(); + while (st.hasMoreElements()) + { + String name = st.nextToken(); + int start = Integer.parseInt(st.nextToken()); + int end = Integer.parseInt(st.nextToken()); + seqs.addElement(new Sequence(name, st.nextToken(), start, end)); + } + SequenceI[] newSeqs = new SequenceI[seqs.size()]; + for (int i = 0; i < seqs.size(); i++) + { + newSeqs[i] = (SequenceI) seqs.elementAt(i); + } + + if (newAlignment) + { + String newtitle = new String("Copied sequences"); + if (getTitle().startsWith("Copied sequences")) + { + newtitle = getTitle(); + } + else + { + newtitle = newtitle.concat("- from " + getTitle()); + } + AlignFrame af = new AlignFrame(new Alignment(newSeqs), + viewport.applet, + newtitle, + false); + if (copiedHiddenColumns != null) + { + for (int i = 0; i < copiedHiddenColumns.size(); i++) + { + int[] region = (int[]) copiedHiddenColumns.elementAt(i); + af.viewport.hideColumns(region[0], region[1]); + } + } + + jalview.bin.JalviewLite.addFrame(af, newtitle, DEFAULT_WIDTH, + DEFAULT_HEIGHT); + } + else + { + addSequences(newSeqs); + } + + } + catch (Exception ex) + {} // could be anything being pasted in here + + } + + void addSequences(SequenceI[] seqs) + { + for (int i = 0; i < seqs.length; i++) + { + viewport.alignment.addSequence(seqs[i]); + } + + //!newAlignment + addHistoryItem(new EditCommand( + "Add sequences", + EditCommand.PASTE, + seqs, + 0, + viewport.alignment.getWidth(), + viewport.alignment) + ); + + viewport.setEndSeq(viewport.alignment.getHeight()); + viewport.alignment.getWidth(); + viewport.firePropertyChange("alignment", null, + viewport.alignment.getSequences()); + + } + + protected void cut_actionPerformed() + { + copy_actionPerformed(); + delete_actionPerformed(); + } + + protected void delete_actionPerformed() + { + + SequenceGroup sg = viewport.getSelectionGroup(); + if (sg == null) + { + return; + } + + Vector seqs = new Vector(); + SequenceI seq; + for (int i = 0; i < sg.getSize(); i++) + { + seq = sg.getSequenceAt(i); + seqs.addElement(seq); + } + + // If the cut affects all sequences, remove highlighted columns + if (sg.getSize() == viewport.alignment.getHeight()) + { + viewport.getColumnSelection().removeElements(sg.getStartRes(), + sg.getEndRes() + 1); + } + + SequenceI[] cut = new SequenceI[seqs.size()]; + for (int i = 0; i < seqs.size(); i++) + { + cut[i] = (SequenceI) seqs.elementAt(i); + } + + /* + //ADD HISTORY ITEM + */ + addHistoryItem(new EditCommand("Cut Sequences", + EditCommand.CUT, + cut, + sg.getStartRes(), + sg.getEndRes() - sg.getStartRes() + 1, + viewport.alignment)); + + viewport.setSelectionGroup(null); + viewport.alignment.deleteGroup(sg); + + viewport.firePropertyChange("alignment", null, + viewport.getAlignment().getSequences()); + + if (viewport.getAlignment().getHeight() < 1) + { + this.setVisible(false); + } + } + + protected void deleteGroups_actionPerformed() + { + viewport.alignment.deleteAllGroups(); + viewport.sequenceColours = null; + viewport.setSelectionGroup(null); + + alignPanel.paintAlignment(true); + } + + public void selectAllSequenceMenuItem_actionPerformed() + { + SequenceGroup sg = new SequenceGroup(); + for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++) + { + sg.addSequence(viewport.getAlignment().getSequenceAt(i), false); + } + sg.setEndRes(viewport.alignment.getWidth() - 1); + viewport.setSelectionGroup(sg); + alignPanel.paintAlignment(true); + PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId()); + } + + public void deselectAllSequenceMenuItem_actionPerformed() + { + if (viewport.cursorMode) + { + alignPanel.seqPanel.keyboardNo1 = null; + alignPanel.seqPanel.keyboardNo2 = null; + } + viewport.setSelectionGroup(null); + viewport.getColumnSelection().clear(); + viewport.setSelectionGroup(null); + alignPanel.idPanel.idCanvas.searchResults = null; + alignPanel.seqPanel.seqCanvas.highlightSearchResults(null); + alignPanel.paintAlignment(true); + PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId()); + } + + public void invertSequenceMenuItem_actionPerformed() + { + SequenceGroup sg = viewport.getSelectionGroup(); + for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++) + { + sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false); + } + + PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId()); + } + + void trimAlignment(boolean trimLeft) + { + ColumnSelection colSel = viewport.getColumnSelection(); + int column; + + if (colSel.size() > 0) + { + if (trimLeft) + { + column = colSel.getMin(); + } + else + { + column = colSel.getMax(); + } + + SequenceI[] seqs; + if (viewport.getSelectionGroup() != null) + { + seqs = viewport.getSelectionGroup().getSequencesAsArray(viewport. + hiddenRepSequences); + } + else + { + seqs = viewport.alignment.getSequencesArray(); + } + + TrimRegionCommand trimRegion; + if (trimLeft) + { + trimRegion = new TrimRegionCommand("Remove Left", + TrimRegionCommand.TRIM_LEFT, + seqs, + column, + viewport.alignment, + viewport.colSel, + viewport.selectionGroup); + viewport.setStartRes(0); + } + else + { + trimRegion = new TrimRegionCommand("Remove Right", + TrimRegionCommand.TRIM_RIGHT, + seqs, + column, + viewport.alignment, + viewport.colSel, + viewport.selectionGroup); + } + + statusBar.setText("Removed " + trimRegion.getSize() + " columns."); + + addHistoryItem(trimRegion); + + Vector groups = viewport.alignment.getGroups(); + + for (int i = 0; i < groups.size(); i++) + { + SequenceGroup sg = (SequenceGroup) groups.elementAt(i); + + if ( (trimLeft && !sg.adjustForRemoveLeft(column)) + || (!trimLeft && !sg.adjustForRemoveRight(column))) + { + viewport.alignment.deleteGroup(sg); + } + } + + viewport.firePropertyChange("alignment", null, + viewport.getAlignment().getSequences()); + } + } + + public void removeGappedColumnMenuItem_actionPerformed() + { + int start = 0, end = viewport.alignment.getWidth() - 1; + + SequenceI[] seqs; + if (viewport.getSelectionGroup() != null) + { + seqs = viewport.getSelectionGroup().getSequencesAsArray(viewport. + hiddenRepSequences); + start = viewport.getSelectionGroup().getStartRes(); + end = viewport.getSelectionGroup().getEndRes(); + } + else + { + seqs = viewport.alignment.getSequencesArray(); + } + + RemoveGapColCommand removeGapCols = + new RemoveGapColCommand("Remove Gapped Columns", + seqs, + start, end, + viewport.alignment); + + addHistoryItem(removeGapCols); + + statusBar.setText("Removed " + removeGapCols.getSize() + " empty columns."); + + //This is to maintain viewport position on first residue + //of first sequence + SequenceI seq = viewport.alignment.getSequenceAt(0); + int startRes = seq.findPosition(viewport.startRes); + // ShiftList shifts; + // viewport.getAlignment().removeGaps(shifts=new ShiftList()); + // edit.alColumnChanges=shifts.getInverse(); + // if (viewport.hasHiddenColumns) + // viewport.getColumnSelection().compensateForEdits(shifts); + viewport.setStartRes(seq.findIndex(startRes) - 1); + viewport.firePropertyChange("alignment", null, + viewport.getAlignment().getSequences()); + + } + + public void removeAllGapsMenuItem_actionPerformed() + { + int start = 0, end = viewport.alignment.getWidth() - 1; + + SequenceI[] seqs; + if (viewport.getSelectionGroup() != null) + { + seqs = viewport.getSelectionGroup().getSequencesAsArray(viewport. + hiddenRepSequences); + start = viewport.getSelectionGroup().getStartRes(); + end = viewport.getSelectionGroup().getEndRes(); + } + else + { + seqs = viewport.alignment.getSequencesArray(); + } + + //This is to maintain viewport position on first residue + //of first sequence + SequenceI seq = viewport.alignment.getSequenceAt(0); + int startRes = seq.findPosition(viewport.startRes); + + addHistoryItem(new RemoveGapsCommand("Remove Gaps", + seqs, + start, end, + viewport.alignment)); + + viewport.setStartRes(seq.findIndex(startRes) - 1); + + viewport.firePropertyChange("alignment", null, + viewport.getAlignment().getSequences()); + + } + + public void findMenuItem_actionPerformed() + { + new Finder(alignPanel); + } + + public void newView() + { + AlignmentI newal; + if (viewport.hasHiddenRows) + { + newal = new Alignment(viewport.getAlignment(). + getHiddenSequences() + .getFullAlignment(). + getSequencesArray()); + } + else + { + newal = new Alignment(viewport.alignment.getSequencesArray()); + } + + if (viewport.alignment.getAlignmentAnnotation() != null) + { + for (int i = 0; i < viewport.alignment.getAlignmentAnnotation().length; i++) + { + if (!viewport.alignment.getAlignmentAnnotation()[i].autoCalculated) + { + newal.addAnnotation(viewport.alignment.getAlignmentAnnotation()[i]); + } + } + } + + AlignFrame newaf = new AlignFrame(newal, + viewport.applet, + "", + false); + + newaf.viewport.sequenceSetID = alignPanel.av.getSequenceSetId(); + PaintRefresher.Register(alignPanel, alignPanel.av.getSequenceSetId()); + PaintRefresher.Register(newaf.alignPanel, + newaf.alignPanel.av.getSequenceSetId()); + + PaintRefresher.Register(newaf.alignPanel.idPanel.idCanvas, + newaf.alignPanel.av.getSequenceSetId()); + PaintRefresher.Register(newaf.alignPanel.seqPanel.seqCanvas, + newaf.alignPanel.av.getSequenceSetId()); + + Vector comps = (Vector) PaintRefresher.components.get(viewport. + getSequenceSetId()); + int viewSize = -1; + for (int i = 0; i < comps.size(); i++) + { + if (comps.elementAt(i) instanceof AlignmentPanel) + { + viewSize++; + } + } + + String title = new String(this.getTitle()); + if (title.indexOf("(View") > -1) + { + title = title.substring(0, title.indexOf("(View")); + } + + title += "(View " + viewSize + ")"; + + newaf.setTitle(title.toString()); + + newaf.viewport.historyList = viewport.historyList; + newaf.viewport.redoList = viewport.redoList; + + } + + public void seqLimits_itemStateChanged() + { + viewport.setShowJVSuffix(seqLimits.getState()); + alignPanel.fontChanged(); + alignPanel.paintAlignment(true); + } + + protected void colourTextMenuItem_actionPerformed() + { + viewport.setColourText(colourTextMenuItem.getState()); + alignPanel.paintAlignment(true); + } + + protected void wrapMenuItem_actionPerformed() + { + viewport.setWrapAlignment(wrapMenuItem.getState()); + alignPanel.setWrapAlignment(wrapMenuItem.getState()); + scaleAbove.setEnabled(wrapMenuItem.getState()); + scaleLeft.setEnabled(wrapMenuItem.getState()); + scaleRight.setEnabled(wrapMenuItem.getState()); + alignPanel.paintAlignment(true); + } + + public void overviewMenuItem_actionPerformed() + { + if (alignPanel.overviewPanel != null) + { + return; + } + + Frame frame = new Frame(); + OverviewPanel overview = new OverviewPanel(alignPanel); + frame.add(overview); + // +50 must allow for applet frame window + jalview.bin.JalviewLite.addFrame(frame, "Overview " + this.getTitle(), + overview.getPreferredSize().width, + overview.getPreferredSize().height + 50); + + frame.pack(); + frame.addWindowListener(new WindowAdapter() + { + public void windowClosing(WindowEvent e) + { + alignPanel.setOverviewPanel(null); + }; + }); + + alignPanel.setOverviewPanel(overview); + + } + + void changeColour(ColourSchemeI cs) + { + int threshold = 0; + + if (cs != null) + { + if (viewport.getAbovePIDThreshold()) + { + threshold = SliderPanel.setPIDSliderSource(alignPanel, cs, "Background"); + + cs.setThreshold(threshold, viewport.getIgnoreGapsConsensus()); + + viewport.setGlobalColourScheme(cs); + } + else + { + cs.setThreshold(0, viewport.getIgnoreGapsConsensus()); + } + + if (viewport.getConservationSelected()) + { + + Alignment al = (Alignment) viewport.alignment; + Conservation c = new Conservation("All", + ResidueProperties.propHash, 3, + al.getSequences(), 0, + al.getWidth() - 1); + + c.calculate(); + c.verdict(false, viewport.ConsPercGaps); + + cs.setConservation(c); + + cs.setConservationInc(SliderPanel.setConservationSlider(alignPanel, cs, + "Background")); + + } + else + { + cs.setConservation(null); + } + + cs.setConsensus(viewport.hconsensus); + + } + viewport.setGlobalColourScheme(cs); + + if (viewport.getColourAppliesToAllGroups()) + { + Vector groups = viewport.alignment.getGroups(); + for (int i = 0; i < groups.size(); i++) + { + SequenceGroup sg = (SequenceGroup) groups.elementAt(i); + + if (cs == null) + { + sg.cs = null; + continue; + } + if (cs instanceof ClustalxColourScheme) + { + sg.cs = new ClustalxColourScheme( + sg.getSequences(viewport.hiddenRepSequences), + sg.getWidth()); + } + else + { + try + { + sg.cs = (ColourSchemeI) cs.getClass().newInstance(); + } + catch (Exception ex) + { + ex.printStackTrace(); + sg.cs = cs; + } + } + + if (viewport.getAbovePIDThreshold() + || cs instanceof PIDColourScheme + || cs instanceof Blosum62ColourScheme) + { + sg.cs.setThreshold(threshold, viewport.getIgnoreGapsConsensus()); + sg.cs.setConsensus(AAFrequency.calculate( + sg.getSequences(viewport.hiddenRepSequences), 0, sg.getWidth())); + } + else + { + sg.cs.setThreshold(0, viewport.getIgnoreGapsConsensus()); + } + + if (viewport.getConservationSelected()) + { + Conservation c = new Conservation("Group", + ResidueProperties.propHash, 3, + sg.getSequences(viewport. + hiddenRepSequences), 0, + viewport.alignment.getWidth() - 1); + c.calculate(); + c.verdict(false, viewport.ConsPercGaps); + sg.cs.setConservation(c); + } + else + { + sg.cs.setConservation(null); + sg.cs.setThreshold(0, viewport.getIgnoreGapsConsensus()); + } + + } + } + + if (alignPanel.getOverviewPanel() != null) + { + alignPanel.getOverviewPanel().updateOverviewImage(); + } + + jalview.structure.StructureSelectionManager.getStructureSelectionManager() + .sequenceColoursChanged(alignPanel); + + alignPanel.paintAlignment(true); + } + + protected void modifyPID_actionPerformed() + { + if (viewport.getAbovePIDThreshold() && viewport.globalColourScheme != null) + { + SliderPanel.setPIDSliderSource(alignPanel, viewport.getGlobalColourScheme(), + "Background"); + SliderPanel.showPIDSlider(); + } + } + + protected void modifyConservation_actionPerformed() + { + if (viewport.getConservationSelected() && viewport.globalColourScheme != null) + { + SliderPanel.setConservationSlider(alignPanel, viewport.globalColourScheme, + "Background"); + SliderPanel.showConservationSlider(); + } + } + + protected void conservationMenuItem_actionPerformed() + { + viewport.setConservationSelected(conservationMenuItem.getState()); + + viewport.setAbovePIDThreshold(false); + abovePIDThreshold.setState(false); + + changeColour(viewport.getGlobalColourScheme()); + + modifyConservation_actionPerformed(); + } + + public void abovePIDThreshold_actionPerformed() + { + viewport.setAbovePIDThreshold(abovePIDThreshold.getState()); + + conservationMenuItem.setState(false); + viewport.setConservationSelected(false); + + changeColour(viewport.getGlobalColourScheme()); + + modifyPID_actionPerformed(); + } + + public void sortPairwiseMenuItem_actionPerformed() + { + SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray(); + AlignmentSorter.sortByPID(viewport.getAlignment(), + viewport.getAlignment().getSequenceAt(0)); + addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder, + viewport.alignment)); + alignPanel.paintAlignment(true); + } + + public void sortIDMenuItem_actionPerformed() + { + // addHistoryItem(new HistoryItem("ID Sort", viewport.alignment, + // HistoryItem.SORT)); + AlignmentSorter.sortByID(viewport.getAlignment()); + alignPanel.paintAlignment(true); + } + + public void sortGroupMenuItem_actionPerformed() + { + // addHistoryItem(new HistoryItem("Group Sort", viewport.alignment, + // HistoryItem.SORT)); + AlignmentSorter.sortByGroup(viewport.getAlignment()); + alignPanel.paintAlignment(true); + + } + + public void removeRedundancyMenuItem_actionPerformed() + { + new RedundancyPanel(alignPanel); + } + + public void pairwiseAlignmentMenuItem_actionPerformed() + { + if (viewport.getSelectionGroup() != null + && viewport.getSelectionGroup().getSize() > 1) + { + Frame frame = new Frame(); + frame.add(new PairwiseAlignPanel(alignPanel)); + jalview.bin.JalviewLite.addFrame(frame, "Pairwise Alignment", 600, 500); + } + } + + public void PCAMenuItem_actionPerformed() + { + //are the sequences aligned? + if (!viewport.alignment.isAligned()) + { + SequenceI current; + int Width = viewport.getAlignment().getWidth(); + + for (int i = 0; i < viewport.getAlignment().getSequences().size(); + i++) + { + current = viewport.getAlignment().getSequenceAt(i); + + if (current.getLength() < Width) + { + current.insertCharAt(Width - 1, viewport.getGapCharacter()); + } + } + alignPanel.paintAlignment(true); + } + + if ( (viewport.getSelectionGroup() != null && + viewport.getSelectionGroup().getSize() < 4 && + viewport.getSelectionGroup().getSize() > 0) + || viewport.getAlignment().getHeight() < 4) + { + return; + } + + try + { + new PCAPanel(viewport); + } + catch (java.lang.OutOfMemoryError ex) + { + } + + } + + public void averageDistanceTreeMenuItem_actionPerformed() + { + NewTreePanel("AV", "PID", "Average distance tree using PID"); + } + + public void neighbourTreeMenuItem_actionPerformed() + { + NewTreePanel("NJ", "PID", "Neighbour joining tree using PID"); + } + + protected void njTreeBlosumMenuItem_actionPerformed() + { + NewTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62"); + } + + protected void avTreeBlosumMenuItem_actionPerformed() + { + NewTreePanel("AV", "BL", "Average distance tree using BLOSUM62"); + } + + void NewTreePanel(String type, String pwType, String title) + { + //are the sequences aligned? + if (!viewport.alignment.isAligned()) + { + SequenceI current; + int Width = viewport.getAlignment().getWidth(); + + for (int i = 0; i < viewport.getAlignment().getSequences().size(); + i++) + { + current = viewport.getAlignment().getSequenceAt(i); + + if (current.getLength() < Width) + { + current.insertCharAt(Width - 1, viewport.getGapCharacter()); + } + } + alignPanel.paintAlignment(true); + + } + + if ( (viewport.getSelectionGroup() != null && + viewport.getSelectionGroup().getSize() > 1) + || (viewport.getSelectionGroup() == null + && viewport.alignment.getHeight() > 1)) + { + final TreePanel tp = new TreePanel(viewport, + type, + pwType); + + addTreeMenuItem(tp, title); + + jalview.bin.JalviewLite.addFrame(tp, title, 600, 500); + } + } + + void loadTree_actionPerformed() + { + CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this); + cap.setText("Paste your Newick tree file here."); + cap.setTreeImport(); + Frame frame = new Frame(); + frame.add(cap); + jalview.bin.JalviewLite.addFrame(frame, "Paste Newick file ", 400, 300); + } + + public void loadTree(jalview.io.NewickFile tree, String treeFile) + { + TreePanel tp = new TreePanel(viewport, + treeFile, + "From File - ", + tree); + jalview.bin.JalviewLite.addFrame(tp, treeFile, 600, 500); + addTreeMenuItem(tp, treeFile); + } + + 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.paintAlignment(true); + } + }); + + 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 + + MenuBar alignFrameMenuBar = new MenuBar(); + Menu fileMenu = new Menu("File"); + MenuItem loadApplication = new MenuItem("View in Full Application"); + MenuItem loadTree = new MenuItem("Load Associated Tree ..."); + MenuItem loadAnnotations = new MenuItem( + "Load Features/Annotations ..."); + MenuItem outputFeatures = new MenuItem("Export Features ..."); + MenuItem outputAnnotations = new MenuItem("Export Annotations ..."); + + MenuItem closeMenuItem = new MenuItem("Close"); + Menu editMenu = new Menu("Edit"); + Menu viewMenu = new Menu("View"); + Menu colourMenu = new Menu("Colour"); + Menu calculateMenu = new Menu("Calculate"); + MenuItem selectAllSequenceMenuItem = new MenuItem("Select all"); + MenuItem deselectAllSequenceMenuItem = new MenuItem("Deselect All"); + MenuItem invertSequenceMenuItem = new MenuItem("Invert Selection"); + MenuItem remove2LeftMenuItem = new MenuItem(); + MenuItem remove2RightMenuItem = new MenuItem(); + MenuItem removeGappedColumnMenuItem = new MenuItem(); + MenuItem removeAllGapsMenuItem = new MenuItem(); + CheckboxMenuItem viewBoxesMenuItem = new CheckboxMenuItem(); + CheckboxMenuItem viewTextMenuItem = new CheckboxMenuItem(); + MenuItem sortPairwiseMenuItem = new MenuItem(); + MenuItem sortIDMenuItem = new MenuItem(); + MenuItem sortGroupMenuItem = new MenuItem(); + MenuItem removeRedundancyMenuItem = new MenuItem(); + MenuItem pairwiseAlignmentMenuItem = new MenuItem(); + MenuItem PCAMenuItem = new MenuItem(); + MenuItem averageDistanceTreeMenuItem = new MenuItem(); + MenuItem neighbourTreeMenuItem = new MenuItem(); + BorderLayout borderLayout1 = new BorderLayout(); + public Label statusBar = new Label(); + Menu outputTextboxMenu = new Menu(); + MenuItem clustalColour = new MenuItem(); + MenuItem zappoColour = new MenuItem(); + MenuItem taylorColour = new MenuItem(); + MenuItem hydrophobicityColour = new MenuItem(); + MenuItem helixColour = new MenuItem(); + MenuItem strandColour = new MenuItem(); + MenuItem turnColour = new MenuItem(); + MenuItem buriedColour = new MenuItem(); + MenuItem userDefinedColour = new MenuItem(); + MenuItem PIDColour = new MenuItem(); + MenuItem BLOSUM62Colour = new MenuItem(); + MenuItem njTreeBlosumMenuItem = new MenuItem(); + MenuItem avDistanceTreeBlosumMenuItem = new MenuItem(); + CheckboxMenuItem annotationPanelMenuItem = new CheckboxMenuItem(); + CheckboxMenuItem colourTextMenuItem = new CheckboxMenuItem(); + MenuItem alProperties = new MenuItem("Alignment Properties..."); + MenuItem overviewMenuItem = new MenuItem(); + MenuItem undoMenuItem = new MenuItem(); + MenuItem redoMenuItem = new MenuItem(); + CheckboxMenuItem conservationMenuItem = new CheckboxMenuItem(); + MenuItem noColourmenuItem = new MenuItem(); + CheckboxMenuItem wrapMenuItem = new CheckboxMenuItem(); + CheckboxMenuItem renderGapsMenuItem = new CheckboxMenuItem(); + MenuItem findMenuItem = new MenuItem(); + CheckboxMenuItem abovePIDThreshold = new CheckboxMenuItem(); + MenuItem nucleotideColour = new MenuItem(); + MenuItem deleteGroups = new MenuItem(); + MenuItem delete = new MenuItem(); + MenuItem copy = new MenuItem(); + MenuItem cut = new MenuItem(); + Menu pasteMenu = new Menu(); + MenuItem pasteNew = new MenuItem(); + MenuItem pasteThis = new MenuItem(); + CheckboxMenuItem applyToAllGroups = new CheckboxMenuItem(); + MenuItem font = new MenuItem(); + CheckboxMenuItem scaleAbove = new CheckboxMenuItem(); + CheckboxMenuItem scaleLeft = new CheckboxMenuItem(); + CheckboxMenuItem scaleRight = new CheckboxMenuItem(); + MenuItem modifyPID = new MenuItem(); + MenuItem modifyConservation = new MenuItem(); + CheckboxMenuItem autoCalculate + = new CheckboxMenuItem("Autocalculate Consensus", true); + Menu sortByTreeMenu = new Menu(); + Menu sort = new Menu(); + Menu calculate = new Menu(); + MenuItem inputText = new MenuItem(); + Menu helpMenu = new Menu(); + MenuItem documentation = new MenuItem(); + MenuItem about = new MenuItem(); + CheckboxMenuItem seqLimits = new CheckboxMenuItem(); + Panel embeddedMenu; + Label embeddedEdit; + Label embeddedSelect; + Label embeddedView; + Label embeddedFormat; + 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); + loadAnnotations.addActionListener(this); + outputFeatures.addActionListener(this); + outputAnnotations.addActionListener(this); + selectAllSequenceMenuItem.addActionListener(this); + deselectAllSequenceMenuItem.addActionListener(this); + invertSequenceMenuItem.addActionListener(this); + remove2LeftMenuItem.setLabel("Remove Left"); + remove2LeftMenuItem.addActionListener(this); + remove2RightMenuItem.setLabel("Remove Right"); + remove2RightMenuItem.addActionListener(this); + removeGappedColumnMenuItem.setLabel("Remove Empty Columns"); + removeGappedColumnMenuItem.addActionListener(this); + removeAllGapsMenuItem.setLabel("Remove All Gaps"); + removeAllGapsMenuItem.addActionListener(this); + viewBoxesMenuItem.setLabel("Boxes"); + viewBoxesMenuItem.setState(true); + viewBoxesMenuItem.addItemListener(this); + viewTextMenuItem.setLabel("Text"); + viewTextMenuItem.setState(true); + viewTextMenuItem.addItemListener(this); + sortPairwiseMenuItem.setLabel("by Pairwise Identity"); + sortPairwiseMenuItem.addActionListener(this); + sortIDMenuItem.setLabel("by ID"); + sortIDMenuItem.addActionListener(this); + sortGroupMenuItem.setLabel("by Group"); + sortGroupMenuItem.addActionListener(this); + removeRedundancyMenuItem.setLabel("Remove Redundancy..."); + removeRedundancyMenuItem.addActionListener(this); + pairwiseAlignmentMenuItem.setLabel("Pairwise Alignments..."); + pairwiseAlignmentMenuItem.addActionListener(this); + PCAMenuItem.setLabel("Principal Component Analysis"); + PCAMenuItem.addActionListener(this); + averageDistanceTreeMenuItem.setLabel( + "Average Distance Using % Identity"); + averageDistanceTreeMenuItem.addActionListener(this); + neighbourTreeMenuItem.setLabel("Neighbour Joining Using % Identity"); + neighbourTreeMenuItem.addActionListener(this); + statusBar.setBackground(Color.white); + statusBar.setFont(new java.awt.Font("Verdana", 0, 11)); + statusBar.setText("Status bar"); + outputTextboxMenu.setLabel("Output to Textbox"); + clustalColour.setLabel("Clustalx"); + + clustalColour.addActionListener(this); + zappoColour.setLabel("Zappo"); + zappoColour.addActionListener(this); + taylorColour.setLabel("Taylor"); + taylorColour.addActionListener(this); + hydrophobicityColour.setLabel("Hydrophobicity"); + hydrophobicityColour.addActionListener(this); + helixColour.setLabel("Helix Propensity"); + helixColour.addActionListener(this); + strandColour.setLabel("Strand Propensity"); + strandColour.addActionListener(this); + turnColour.setLabel("Turn Propensity"); + turnColour.addActionListener(this); + buriedColour.setLabel("Buried Index"); + buriedColour.addActionListener(this); + userDefinedColour.setLabel("User Defined..."); + userDefinedColour.addActionListener(this); + PIDColour.setLabel("Percentage Identity"); + PIDColour.addActionListener(this); + BLOSUM62Colour.setLabel("BLOSUM62 Score"); + BLOSUM62Colour.addActionListener(this); + avDistanceTreeBlosumMenuItem.setLabel( + "Average Distance Using BLOSUM62"); + avDistanceTreeBlosumMenuItem.addActionListener(this); + njTreeBlosumMenuItem.setLabel("Neighbour Joining Using BLOSUM62"); + njTreeBlosumMenuItem.addActionListener(this); + annotationPanelMenuItem.setLabel("Show Annotations"); + annotationPanelMenuItem.addItemListener(this); + colourTextMenuItem.setLabel("Colour Text"); + colourTextMenuItem.addItemListener(this); + alProperties.addActionListener(this); + overviewMenuItem.setLabel("Overview Window"); + overviewMenuItem.addActionListener(this); + undoMenuItem.setEnabled(false); + undoMenuItem.setLabel("Undo"); + undoMenuItem.addActionListener(this); + redoMenuItem.setEnabled(false); + redoMenuItem.setLabel("Redo"); + redoMenuItem.addActionListener(this); + conservationMenuItem.setLabel("by Conservation"); + conservationMenuItem.addItemListener(this); + noColourmenuItem.setLabel("None"); + noColourmenuItem.addActionListener(this); + wrapMenuItem.setLabel("Wrap"); + wrapMenuItem.addItemListener(this); + renderGapsMenuItem.setLabel("Show Gaps"); + renderGapsMenuItem.setState(true); + renderGapsMenuItem.addItemListener(this); + findMenuItem.setLabel("Find..."); + findMenuItem.addActionListener(this); + abovePIDThreshold.setLabel("Above Identity Threshold"); + abovePIDThreshold.addItemListener(this); + nucleotideColour.setLabel("Nucleotide"); + nucleotideColour.addActionListener(this); + deleteGroups.setLabel("Undefine Groups"); + deleteGroups.addActionListener(this); + 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); + formatMenu.setLabel("Format"); + selectMenu.setLabel("Select"); + newView.setLabel("New View"); + newView.addActionListener(this); + alignFrameMenuBar.add(fileMenu); + alignFrameMenuBar.add(editMenu); + alignFrameMenuBar.add(selectMenu); + alignFrameMenuBar.add(viewMenu); + alignFrameMenuBar.add(formatMenu); + alignFrameMenuBar.add(colourMenu); + alignFrameMenuBar.add(calculateMenu); + alignFrameMenuBar.add(helpMenu); + + fileMenu.add(inputText); + fileMenu.add(loadTree); + fileMenu.add(loadAnnotations); + + fileMenu.addSeparator(); + fileMenu.add(outputTextboxMenu); + fileMenu.add(outputFeatures); + fileMenu.add(outputAnnotations); + + if (jalviewServletURL != null) + { + fileMenu.add(loadApplication); + } + + fileMenu.addSeparator(); + fileMenu.add(closeMenuItem); + + editMenu.add(undoMenuItem); + editMenu.add(redoMenuItem); + editMenu.add(cut); + editMenu.add(copy); + editMenu.add(pasteMenu); + editMenu.add(delete); + editMenu.addSeparator(); + editMenu.add(remove2LeftMenuItem); + editMenu.add(remove2RightMenuItem); + editMenu.add(removeGappedColumnMenuItem); + editMenu.add(removeAllGapsMenuItem); + editMenu.add(removeRedundancyMenuItem); + viewMenu.add(newView); + viewMenu.addSeparator(); + viewMenu.add(menu1); + viewMenu.add(menu2); + viewMenu.addSeparator(); + viewMenu.add(annotationPanelMenuItem); + viewMenu.addSeparator(); + viewMenu.add(sequenceFeatures); + viewMenu.add(featureSettings); + viewMenu.addSeparator(); + viewMenu.add(alProperties); + viewMenu.addSeparator(); + viewMenu.add(overviewMenuItem); + colourMenu.add(applyToAllGroups); + colourMenu.addSeparator(); + colourMenu.add(noColourmenuItem); + colourMenu.add(clustalColour); + colourMenu.add(BLOSUM62Colour); + colourMenu.add(PIDColour); + colourMenu.add(zappoColour); + colourMenu.add(taylorColour); + colourMenu.add(hydrophobicityColour); + colourMenu.add(helixColour); + colourMenu.add(strandColour); + colourMenu.add(turnColour); + colourMenu.add(buriedColour); + colourMenu.add(nucleotideColour); + colourMenu.add(userDefinedColour); + colourMenu.addSeparator(); + colourMenu.add(conservationMenuItem); + colourMenu.add(modifyConservation); + colourMenu.add(abovePIDThreshold); + colourMenu.add(modifyPID); + colourMenu.add(annotationColour); + calculateMenu.add(sort); + calculateMenu.add(calculate); + calculateMenu.addSeparator(); + calculateMenu.add(pairwiseAlignmentMenuItem); + calculateMenu.add(PCAMenuItem); + calculateMenu.add(autoCalculate); + this.add(statusBar, BorderLayout.SOUTH); + pasteMenu.add(pasteNew); + pasteMenu.add(pasteThis); + sort.add(sortIDMenuItem); + sort.add(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); + formatMenu.add(font); + formatMenu.add(seqLimits); + formatMenu.add(wrapMenuItem); + formatMenu.add(scaleAbove); + formatMenu.add(scaleLeft); + formatMenu.add(scaleRight); + formatMenu.add(viewBoxesMenuItem); + formatMenu.add(viewTextMenuItem); + formatMenu.add(colourTextMenuItem); + formatMenu.add(renderGapsMenuItem); + selectMenu.add(findMenuItem); + selectMenu.addSeparator(); + selectMenu.add(selectAllSequenceMenuItem); + selectMenu.add(deselectAllSequenceMenuItem); + selectMenu.add(invertSequenceMenuItem); + selectMenu.add(invertColSel); + selectMenu.add(deleteGroups); + } + + public void setEmbedded() + { + + embeddedMenu = new Panel(); + embeddedEdit = new Label("Edit"); + embeddedSelect = new Label("Select"); + embeddedView = new Label("View"); + embeddedFormat = new Label("Format"); + embeddedColour = new Label("Colour"); + embeddedFile = new Label("File"); + embeddedHelp = new Label("Help"); + embeddedCalculate = new Label("Calculate"); + flowLayout1 = new FlowLayout(); + embeddedMenu.setBackground(Color.lightGray); + embeddedMenu.setLayout(flowLayout1); + embeddedEdit.setFont(new java.awt.Font("Arial", Font.PLAIN, 10)); + embeddedSelect.setFont(new java.awt.Font("Arial", Font.PLAIN, 10)); + embeddedView.setFont(new java.awt.Font("Arial", Font.PLAIN, 10)); + embeddedFormat.setFont(new java.awt.Font("Arial", Font.PLAIN, 10)); + embeddedColour.setFont(new java.awt.Font("Arial", Font.PLAIN, 10)); + embeddedFile.setFont(new java.awt.Font("Arial", Font.PLAIN, 10)); + embeddedHelp.setFont(new java.awt.Font("Arial", Font.PLAIN, 10)); + embeddedCalculate.setFont(new java.awt.Font("Arial", Font.PLAIN, 10)); + embeddedMenu.add(embeddedFile); + embeddedMenu.add(embeddedEdit); + embeddedMenu.add(embeddedSelect); + embeddedMenu.add(embeddedView); + embeddedMenu.add(embeddedFormat); + 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); + embeddedSelect.addMouseListener(this); + embeddedView.addMouseListener(this); + embeddedFormat.addMouseListener(this); + embeddedColour.addMouseListener(this); + embeddedCalculate.addMouseListener(this); + embeddedHelp.addMouseListener(this); + + fileMenu.remove(closeMenuItem); + fileMenu.remove(3); // Seperator + + viewport.applet.setLayout(new BorderLayout()); + viewport.applet.add(embeddedMenu, BorderLayout.NORTH); + viewport.applet.add(statusBar, BorderLayout.SOUTH); + + alignPanel.setSize(viewport.applet.getSize().width, + viewport.applet.getSize().height + - embeddedMenu.HEIGHT - statusBar.HEIGHT); + + viewport.applet.add(alignPanel, BorderLayout.CENTER); + viewport.applet.validate(); + + } + + PopupMenu filePopup, editPopup, searchPopup, + viewPopup, formatPopup, 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(); + Menu formatMenu = new Menu(); + Menu selectMenu = new Menu(); + MenuItem newView = 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 == embeddedSelect) + { + popup = searchPopup = genPopupMenu(searchPopup, selectMenu); + } + else if (source == embeddedView) + { + popup = viewPopup = genPopupMenu(viewPopup, viewMenu); + } + else if (source == embeddedFormat) + { + popup = formatPopup = genPopupMenu(formatPopup, formatMenu); + } + 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 < mSize; m++) + { + popup.add(original.getItem(m)); + mSize--; + m--; + } + + return popup; + } + + public void mouseClicked(MouseEvent evt) + {} + + public void mouseReleased(MouseEvent evt) + {} + + public void mouseEntered(MouseEvent evt) + {} + + public void mouseExited(MouseEvent evt) + {} + +}