X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignFrame.java;h=bfbc969705ac06ca93a534ae3030eb5e63201b04;hb=68ba1a55efa08e12e4381bb0e5bdcb70318e1dd5;hp=90e911ef6c8472f9e2409b71e780af1f7eab3c99;hpb=f24dacb1da56fccf05d684e2f4899facec2aecf7;p=jalview.git diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java old mode 100755 new mode 100644 index 90e911e..bfbc969 --- a/src/jalview/gui/AlignFrame.java +++ b/src/jalview/gui/AlignFrame.java @@ -1,2367 +1,6187 @@ -/* - * 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 Softwarechang - * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA - */ -package jalview.gui; - -import java.beans.*; -import java.io.*; -import java.util.*; - -import java.awt.*; -import java.awt.datatransfer.*; -import java.awt.event.*; -import java.awt.print.*; -import javax.swing.*; - -import jalview.analysis.*; -import jalview.datamodel.*; -import jalview.io.*; -import jalview.jbgui.*; -import jalview.schemes.*; -import jalview.ws.*; - -/** - * DOCUMENT ME! - * - * @author $author$ - * @version $Revision$ - */ -public class AlignFrame - extends GAlignFrame -{ - /** DOCUMENT ME!! */ - public static final int NEW_WINDOW_WIDTH = 700; - - /** DOCUMENT ME!! */ - public static final int NEW_WINDOW_HEIGHT = 500; - final AlignmentPanel alignPanel; - final AlignViewport viewport; - - /** DOCUMENT ME!! */ - public String currentFileFormat = null; - Stack historyList = new Stack(); - Stack redoList = new Stack(); - private int treeCount = 0; - - /** - * Creates a new AlignFrame object. - * - * @param al DOCUMENT ME! - */ - public AlignFrame(AlignmentI al) - { - viewport = new AlignViewport(al); - - if(viewport.vconsensus==null) - { - //Out of memory caluclating consensus. - BLOSUM62Colour.setEnabled(false); - PIDColour.setEnabled(false); - conservationMenuItem.setEnabled(false); - modifyConservation.setEnabled(false); - abovePIDThreshold.setEnabled(false); - modifyPID.setEnabled(false); - } - - alignPanel = new AlignmentPanel(this, viewport); - alignPanel.annotationPanel.adjustPanelHeight(); - alignPanel.annotationSpaceFillerHolder.setPreferredSize(alignPanel. - annotationPanel.getPreferredSize()); - alignPanel.annotationScroller.setPreferredSize(alignPanel.annotationPanel. - getPreferredSize()); - alignPanel.setAnnotationVisible(viewport.getShowAnnotation()); - - String sortby = jalview.bin.Cache.getDefault("SORT_ALIGNMENT", "No sort"); - - if(sortby.equals("Id")) - sortIDMenuItem_actionPerformed(null); - else if(sortby.equals("Pairwise Identity")) - sortPairwiseMenuItem_actionPerformed(null); - - getContentPane().add(alignPanel, java.awt.BorderLayout.CENTER); - - viewport.addPropertyChangeListener(new PropertyChangeListener() - { - public void propertyChange(PropertyChangeEvent evt) - { - if (evt.getPropertyName().equals("alignment")) - { - alignmentChanged(); - } - } - }); - - if(Desktop.desktop!=null) - addServiceListeners(); - } - - /* Set up intrinsic listeners for dynamically generated GUI bits. */ - private void addServiceListeners() - { - final java.beans.PropertyChangeListener thisListener; - // Do this once to get current state - BuildWebServiceMenu(); - Desktop.discoverer.addPropertyChangeListener( - thisListener = new java.beans.PropertyChangeListener() - { - public void propertyChange(PropertyChangeEvent evt) - { - // System.out.println("Discoverer property change."); - if (evt.getPropertyName().equals("services")) - { - // System.out.println("Rebuilding web service menu"); - BuildWebServiceMenu(); - } - } - }); - addInternalFrameListener(new javax.swing.event. - InternalFrameAdapter() - { - public void internalFrameClosed( - javax.swing.event.InternalFrameEvent evt) - { - // System.out.println("deregistering discoverer listener"); - Desktop.discoverer.removePropertyChangeListener(thisListener); - closeMenuItem_actionPerformed(null); - } - ; - }); - - } - - /** - * DOCUMENT ME! - * - * @param String DOCUMENT ME! - */ - - public void parseGroupsFile(String file) - { - try - { - BufferedReader in = new BufferedReader(new FileReader(file)); - SequenceI seq = null; - String line, text, token; - UserColourScheme ucs; - int index, start, end; - StringTokenizer st; - SequenceGroup sg; - while ( (line = in.readLine()) != null) - { - st = new StringTokenizer(line, "\t"); - if (st.countTokens() != 6) - { - System.out.println("Groups file " + file + - " is invalid. Read help file."); - System.exit(1); - } - - while (st.hasMoreElements()) - { - text = st.nextToken(); - token = st.nextToken(); - if (!token.equals("ID_NOT_SPECIFIED")) - { - index = viewport.alignment.findIndex(viewport.alignment.findName( - token)); - st.nextToken(); - } - else - { - index = Integer.parseInt(st.nextToken()); - } - - start = Integer.parseInt(st.nextToken()); - end = Integer.parseInt(st.nextToken()); - ucs = new UserColourScheme(st.nextToken()); - - seq = viewport.alignment.getSequenceAt(index); - start = seq.findIndex(start) - 1; - end = seq.findIndex(end) - 1; - - sg = new SequenceGroup(text, ucs, true, true, false, start, end); - sg.addSequence(seq, true); - - viewport.alignment.addGroup(sg); - } - } - - } - catch (Exception ex) - { - System.out.println("Error parsing groups file: " + ex); - } - } - - /** - * DOCUMENT ME! - * - * @param e DOCUMENT ME! - */ - public void saveAlignmentMenu_actionPerformed(ActionEvent e) - { - JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache. - getProperty( - "LAST_DIRECTORY"), - new String[] - { - "fa, fasta, fastq", "aln", "pfam", "msf", "pir", "blc", - "jar" - }, - new String[] - { - "Fasta", "Clustal", "PFAM", "MSF", "PIR", "BLC", "Jalview" - }, currentFileFormat); - - chooser.setAcceptAllFileFilterUsed(false); - chooser.setFileView(new JalviewFileView()); - chooser.setDialogTitle("Save Alignment to file"); - chooser.setToolTipText("Save"); - - int value = chooser.showSaveDialog(this); - - if (value == JalviewFileChooser.APPROVE_OPTION) - { - currentFileFormat = chooser.getSelectedFormat(); - - if (currentFileFormat == null) - { - JOptionPane.showInternalMessageDialog(Desktop.desktop, - "You must select a file format before saving!", - "File format not specified", - JOptionPane.WARNING_MESSAGE); - value = chooser.showSaveDialog(this); - return; - } - - jalview.bin.Cache.setProperty("DEFAULT_FILE_FORMAT", - currentFileFormat); - - String choice = chooser.getSelectedFile().getPath(); - jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice); - - saveAlignment(choice, currentFileFormat); - } - } - - public boolean saveAlignment(String file, String format) - { - if (format.equalsIgnoreCase("Jalview")) - { - String shortName = title; - - if (shortName.indexOf(java.io.File.separatorChar) > -1) - { - shortName = shortName.substring(shortName.lastIndexOf( - java.io.File.separatorChar) + 1); - } - - Jalview2XML.SaveAlignment(this, file, shortName); - - // USE Jalview2XML to save this file - return true; - } - else - { - String output = new FormatAdapter().formatSequences(format, - viewport.getAlignment(). - getSequences()); - if (output == null) - { - return false; - } - - try - { - java.io.PrintWriter out = new java.io.PrintWriter( - new java.io.FileWriter(file)); - - out.print(output); - out.close(); - return true; - } - catch (Exception ex) - { - ex.printStackTrace(); - } - } - return false; - } - - /** - * DOCUMENT ME! - * - * @param e DOCUMENT ME! - */ - protected void outputText_actionPerformed(ActionEvent e) - { - CutAndPasteTransfer cap = new CutAndPasteTransfer(); - Desktop.addInternalFrame(cap, - "Alignment output - " + e.getActionCommand(), 600, - 500); - cap.setText(new FormatAdapter().formatSequences(e.getActionCommand(), - viewport.getAlignment(). - getSequences())); - } - - /** - * DOCUMENT ME! - * - * @param e DOCUMENT ME! - */ - protected void htmlMenuItem_actionPerformed(ActionEvent e) - { - new HTMLOutput(viewport); - } - - public void createImageMap(File file, String image) - { - alignPanel.makePNGImageMap(file, image); - } - - /** - * DOCUMENT ME! - * - * @param e DOCUMENT ME! - */ - public void createPNG(File f) - { - alignPanel.makePNG(f); - } - - /** - * DOCUMENT ME! - * - * @param e DOCUMENT ME! - */ - public void createEPS(File f) - { - alignPanel.makeEPS(f); - } - - /** - * DOCUMENT ME! - * - * @param e DOCUMENT ME! - */ - public void printMenuItem_actionPerformed(ActionEvent e) - { - //Putting in a thread avoids Swing painting problems - PrintThread thread = new PrintThread(); - thread.start(); - } - - /** - * DOCUMENT ME! - * - * @param e DOCUMENT ME! - */ - public void closeMenuItem_actionPerformed(ActionEvent e) - { - try - { - PaintRefresher.components.remove(viewport.alignment); - this.setClosed(true); - } - catch (Exception ex) - { - } - } - - /** - * DOCUMENT ME! - */ - void updateEditMenuBar() - { - if (historyList.size() > 0) - { - undoMenuItem.setEnabled(true); - - HistoryItem hi = (HistoryItem) historyList.peek(); - undoMenuItem.setText("Undo " + hi.getDescription()); - } - else - { - undoMenuItem.setEnabled(false); - undoMenuItem.setText("Undo"); - } - - if (redoList.size() > 0) - { - redoMenuItem.setEnabled(true); - - HistoryItem hi = (HistoryItem) redoList.peek(); - redoMenuItem.setText("Redo " + hi.getDescription()); - } - else - { - redoMenuItem.setEnabled(false); - redoMenuItem.setText("Redo"); - } - } - - /** - * DOCUMENT ME! - * - * @param hi DOCUMENT ME! - */ - public void addHistoryItem(HistoryItem hi) - { - historyList.push(hi); - updateEditMenuBar(); - } - - /** - * DOCUMENT ME! - * - * @param e DOCUMENT ME! - */ - 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()); - } - - /** - * DOCUMENT ME! - * - * @param e DOCUMENT ME! - */ - 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) - { - 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()); - } - - /** - * DOCUMENT ME! - * - * @param up DOCUMENT ME! - */ - 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(); - } - - /** - * DOCUMENT ME! - * - * @param e DOCUMENT ME! - */ - protected void copy_actionPerformed(ActionEvent e) - { - if (viewport.getSelectionGroup() == null) - { - System.out.println("null here"); - return; - } - - SequenceGroup sg = viewport.getSelectionGroup(); - - Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard(); - - Hashtable orderedSeqs = new Hashtable(); - SequenceI [] seqs = new SequenceI[sg.getSize()]; - - 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; - } - - seqs[i] = new Sequence(seq.getName(), - seq.getSequence(sg.getStartRes(), sg.getEndRes()+1), - startRes, - endRes); - } - - c.setContents(new StringSelection(FastaFile.print(seqs)), null); - } - - /** - * DOCUMENT ME! - * - * @param e DOCUMENT ME! - */ - protected void pasteNew_actionPerformed(ActionEvent e) - { - paste(true); - } - - /** - * DOCUMENT ME! - * - * @param e DOCUMENT ME! - */ - protected void pasteThis_actionPerformed(ActionEvent e) - { - addHistoryItem(new HistoryItem("Paste Sequences", viewport.alignment, - HistoryItem.PASTE)); - paste(false); - } - - /** - * DOCUMENT ME! - * - * @param newAlignment DOCUMENT ME! - */ - void paste(boolean newAlignment) - { - try - { - Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard(); - Transferable contents = c.getContents(this); - - if (contents == null) - { - return; - } - - String str = (String) contents.getTransferData(DataFlavor.stringFlavor); - - String format = IdentifyFile.Identify(str, "Paste"); - SequenceI[] sequences = new FormatAdapter().readFile(str, "Paste", format); - - - if (newAlignment) - { - AlignFrame af = new AlignFrame(new Alignment(sequences)); - String newtitle = new String("Copied sequences"); - - if (title.startsWith("Copied sequences")) - { - newtitle = title; - } - else - { - newtitle = newtitle.concat("- from " + title); - } - - Desktop.addInternalFrame(af, newtitle, NEW_WINDOW_WIDTH, - NEW_WINDOW_HEIGHT); - } - else - { - //!newAlignment - for (int i = 0; i < sequences.length; i++) - viewport.alignment.addSequence(sequences[i]); - - 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 - } - - - } - - /** - * DOCUMENT ME! - * - * @param e DOCUMENT ME! - */ - protected void cut_actionPerformed(ActionEvent e) - { - copy_actionPerformed(null); - delete_actionPerformed(null); - } - - /** - * DOCUMENT ME! - * - * @param e DOCUMENT ME! - */ - protected void delete_actionPerformed(ActionEvent e) - { - - if (viewport.getSelectionGroup() == null) - { - return; - } - - addHistoryItem(new HistoryItem("Delete Sequences", viewport.alignment, - HistoryItem.HIDE)); - - 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.firePropertyChange("alignment", null, - viewport.getAlignment().getSequences()); - - - - if (viewport.getAlignment().getHeight() < 1) - { - try - { - this.setClosed(true); - } - catch (Exception ex) - { - } - } - } - - /** - * DOCUMENT ME! - * - * @param e DOCUMENT ME! - */ - protected void deleteGroups_actionPerformed(ActionEvent e) - { - viewport.alignment.deleteAllGroups(); - viewport.setSelectionGroup(null); - alignPanel.repaint(); - } - - /** - * DOCUMENT ME! - * - * @param e DOCUMENT ME! - */ - 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); - PaintRefresher.Refresh(null, viewport.alignment); - } - - /** - * DOCUMENT ME! - * - * @param e DOCUMENT ME! - */ - public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e) - { - viewport.setSelectionGroup(null); - viewport.getColumnSelection().clear(); - viewport.setSelectionGroup(null); - alignPanel.annotationPanel.activeRes = null; - PaintRefresher.Refresh(null, viewport.alignment); - } - - /** - * DOCUMENT ME! - * - * @param e DOCUMENT ME! - */ - public void invertSequenceMenuItem_actionPerformed(ActionEvent e) - { - SequenceGroup sg = viewport.getSelectionGroup(); - - if (sg == null) - { - selectAllSequenceMenuItem_actionPerformed(null); - - return; - } - - for (int i = 0; i < viewport.getAlignment().getSequences().size(); - i++) - { - sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false); - } - - PaintRefresher.Refresh(null, viewport.alignment); - } - - /** - * DOCUMENT ME! - * - * @param e DOCUMENT ME! - */ - 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.get(i); - - if (!sg.adjustForRemoveLeft(min)) - { - viewport.alignment.deleteGroup(sg); - } - } - - viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences()); - } - } - - /** - * DOCUMENT ME! - * - * @param e DOCUMENT ME! - */ - 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.get(i); - - if (!sg.adjustForRemoveRight(max)) - { - viewport.alignment.deleteGroup(sg); - } - } - - viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences()); - } - } - - /** - * DOCUMENT ME! - * - * @param e DOCUMENT ME! - */ - 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()); - } - - /** - * DOCUMENT ME! - * - * @param e DOCUMENT ME! - */ - 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; - int 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()+1; - } - else - { - seqs = viewport.alignment.getSequences(); - } - - for (int i = 0; i < seqs.size(); i++) - { - current = (SequenceI) seqs.elementAt(i); - jSize = current.getLength(); - - // Removing a range is much quicker than removing gaps - // one by one for long sequences - int j = start; - int rangeStart=-1, rangeEnd=-1; - - do - { - if (jalview.util.Comparison.isGap(current.getCharAt(j))) - { - if(rangeStart==-1) - { - rangeStart = j; - rangeEnd = j+1; - } - else - { - rangeEnd++; - } - j++; - } - else - { - if(rangeStart>-1) - { - current.deleteChars(rangeStart, rangeEnd); - j-=rangeEnd-rangeStart; - jSize-=rangeEnd-rangeStart; - rangeStart = -1; - rangeEnd = -1; - } - else - j++; - } - } - while (j < end && j < jSize); - if(rangeStart>-1) - { - current.deleteChars(rangeStart, rangeEnd); - } - } - - viewport.setStartRes(seq.findIndex(startRes)-1); - - viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences()); - } - - public void alignmentChanged() - { - if(viewport.vconsensus!=null) - { - viewport.updateConsensus(); - viewport.updateConservation(); - } - resetAllColourSchemes(); - if(alignPanel.overviewPanel!=null) - alignPanel.overviewPanel.updateOverviewImage(); - - 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 0)) || - (viewport.getAlignment().getHeight() < 4)) - { - JOptionPane.showInternalMessageDialog(this, - "Principal component analysis must take\n" + - "at least 4 input sequences.", - "Sequence selection insufficient", - JOptionPane.WARNING_MESSAGE); - - return; - } - - new PCAPanel(viewport); - } - - /** - * DOCUMENT ME! - * - * @param e DOCUMENT ME! - */ - public void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e) - { - NewTreePanel("AV", "PID", "Average distance tree using PID"); - } - - /** - * DOCUMENT ME! - * - * @param e DOCUMENT ME! - */ - public void neighbourTreeMenuItem_actionPerformed(ActionEvent e) - { - NewTreePanel("NJ", "PID", "Neighbour joining tree using PID"); - } - - /** - * DOCUMENT ME! - * - * @param e DOCUMENT ME! - */ - protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e) - { - NewTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62"); - } - - /** - * DOCUMENT ME! - * - * @param e DOCUMENT ME! - */ - protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e) - { - NewTreePanel("AV", "BL", "Average distance tree using BLOSUM62"); - } - - /** - * DOCUMENT ME! - * - * @param type DOCUMENT ME! - * @param pwType DOCUMENT ME! - * @param title DOCUMENT ME! - */ - void NewTreePanel(String type, String pwType, String title) - { - final TreePanel tp; - - if ( (viewport.getSelectionGroup() != null) && - (viewport.getSelectionGroup().getSize() > 3)) - { - int s = 0; - SequenceGroup sg = viewport.getSelectionGroup(); - - /* Decide if the selection is a column region */ - while (s < sg.sequences.size()) - { - if ( ( (SequenceI) sg.sequences.elementAt(s++)).getLength() < - sg.getEndRes()) - { - JOptionPane.showMessageDialog(Desktop.desktop, - "The selected region to create a tree may\nonly contain residues or gaps.\n" + - "Try using the Pad function in the edit menu,\n" + - "or one of the multiple sequence alignment web services.", - "Sequences in selection are not aligned", - JOptionPane.WARNING_MESSAGE); - - return; - } - } - - title = title + " on region"; - tp = new TreePanel(viewport, - viewport.getSelectionGroup().sequences, type, pwType, - sg.getStartRes(), sg.getEndRes()); - } - else - { - //are the sequences aligned? - if (!viewport.alignment.isAligned()) - { - JOptionPane.showMessageDialog(Desktop.desktop, - "The sequences must be aligned before creating a tree.\n" + - "Try using the Pad function in the edit menu,\n" + - "or one of the multiple sequence alignment web services.", - "Sequences not aligned", - JOptionPane.WARNING_MESSAGE); - - return; - } - - tp = new TreePanel(viewport, - viewport.getAlignment().getSequences(), type, pwType, - 0, - viewport.alignment.getWidth()); - } - - addTreeMenuItem(tp, title); - viewport.setCurrentTree(tp.getTree()); - - Desktop.addInternalFrame(tp, title + " from " + this.title, 600, 500); - } - - /** - * DOCUMENT ME! - * - * @param title DOCUMENT ME! - * @param order DOCUMENT ME! - */ - public void addSortByOrderMenuItem(String title, final AlignmentOrder order) - { - final JMenuItem item = new JMenuItem("by " + title); - sort.add(item); - item.addActionListener(new java.awt.event.ActionListener() - { - public void actionPerformed(ActionEvent e) - { - addHistoryItem(new HistoryItem("Sort", viewport.alignment, - HistoryItem.SORT)); - - // TODO: JBPNote - have to map order entries to curent SequenceI pointers - AlignmentSorter.sortBy(viewport.getAlignment(), order); - alignPanel.repaint(); - } - }); - } - - /** - * Maintain the Order by->Displayed Tree menu. - * Creates a new menu item for a TreePanel with an appropriate - * jalview.analysis.AlignmentSorter call. Listeners are added - * to remove the menu item when the treePanel is closed, and adjust - * the tree leaf to sequence mapping when the alignment is modified. - * @param treePanel Displayed tree window. - * @param title SortBy menu item title. - */ - void addTreeMenuItem(final TreePanel treePanel, String title) - { - final JMenuItem item = new JMenuItem(title); - - treeCount++; - - if (treeCount == 1) - { - sort.add(sortByTreeMenu); - } - - sortByTreeMenu.add(item); - item.addActionListener(new java.awt.event.ActionListener() - { - public void actionPerformed(ActionEvent e) - { - addHistoryItem(new HistoryItem("Tree Sort", - viewport.alignment, HistoryItem.SORT)); - AlignmentSorter.sortByTree(viewport.getAlignment(), - treePanel.getTree()); - alignPanel.repaint(); - } - }); - - treePanel.addInternalFrameListener(new javax.swing.event. - InternalFrameAdapter() - { - public void internalFrameClosed( - javax.swing.event.InternalFrameEvent evt) - { - treeCount--; - sortByTreeMenu.remove(item); - - if (treeCount == 0) - { - sort.remove(sortByTreeMenu); - } - } - ; - }); - } - - /** - * Work out whether the whole set of sequences - * or just the selected set will be submitted for multiple alignment. - * - */ - private SequenceI[] gatherSequencesForAlignment() - { - // Now, check we have enough sequences - SequenceI[] msa = null; - - if ( (viewport.getSelectionGroup() != null) && - (viewport.getSelectionGroup().getSize() > 1)) - { - // JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to some common interface! - SequenceGroup seqs = viewport.getSelectionGroup(); - int sz; - msa = new SequenceI[sz = seqs.getSize()]; - - for (int i = 0; i < sz; i++) - { - msa[i] = (SequenceI) seqs.getSequenceAt(i); - } - } - else - { - Vector seqs = viewport.getAlignment().getSequences(); - - if (seqs.size() > 1) - { - msa = new SequenceI[seqs.size()]; - - for (int i = 0; i < seqs.size(); i++) - { - msa[i] = (SequenceI) seqs.elementAt(i); - } - } - } - return msa; - } - - /** - * Decides what is submitted to a secondary structure prediction service, - * the currently selected sequence, or the currently selected alignment - * (where the first sequence in the set is the one that the prediction - * will be for). - */ - SequenceI[] gatherSeqOrMsaForSecStrPrediction() - { - SequenceI seq = null; - SequenceI[] msa = null; - - if ( (viewport.getSelectionGroup() != null) && - (viewport.getSelectionGroup().getSize() > 0)) - { - // JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to some common interface! - SequenceGroup seqs = viewport.getSelectionGroup(); - - if ( (seqs.getSize() == 1) || !viewport.alignment.isAligned()) - { - seq = (SequenceI) seqs.getSequenceAt(0); - } - else - { - int sz; - msa = new SequenceI[sz = seqs.getSize()]; - - for (int i = 0; i < sz; i++) - { - msa[i] = (SequenceI) seqs.getSequenceAt(i); - } - } - } - else - { - Vector seqs = viewport.getAlignment().getSequences(); - - if ( (seqs.size() == 1) || !viewport.alignment.isAligned()) - { - seq = (SequenceI) seqs.elementAt(0); - } - else - { - msa = new SequenceI[seqs.size()]; - - for (int i = 0; i < seqs.size(); i++) - { - msa[i] = (SequenceI) seqs.elementAt(i); - } - } - } - if (msa != null) - { - return msa; - } - else - { - if (seq != null) - { - return new SequenceI[] - { - seq}; - } - } - return null; - } - /** - * DOCUMENT ME! - * - * @param e DOCUMENT ME! - */ - protected void LoadtreeMenuItem_actionPerformed(ActionEvent e) - { - // Pick the tree file - JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache. - getProperty( - "LAST_DIRECTORY")); - chooser.setFileView(new JalviewFileView()); - chooser.setDialogTitle("Select a newick-like tree file"); - chooser.setToolTipText("Load a tree file"); - - int value = chooser.showOpenDialog(null); - - if (value == JalviewFileChooser.APPROVE_OPTION) - { - String choice = chooser.getSelectedFile().getPath(); - jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice); - - try - { - jalview.io.NewickFile fin = new jalview.io.NewickFile(choice, - "File"); - viewport.setCurrentTree(ShowNewickTree(fin, choice).getTree()); - } - catch (Exception ex) - { - JOptionPane.showMessageDialog(Desktop.desktop, - "Problem reading tree file", - ex.getMessage(), - JOptionPane.WARNING_MESSAGE); - ex.printStackTrace(); - } - } - } - - - public TreePanel ShowNewickTree(NewickFile nf, String title) - { - return ShowNewickTree(nf,title,600,500,4,5); - } - /** - * DOCUMENT ME! - * - * @param nf DOCUMENT ME! - * @param title DOCUMENT ME! - * - * @return DOCUMENT ME! - */ - public TreePanel ShowNewickTree(NewickFile nf, String title, int w,int h,int x, int y) - { - TreePanel tp = null; - - try - { - nf.parse(); - - if (nf.getTree() != null) - { - tp = new TreePanel(viewport, - viewport.getAlignment().getSequences(), nf, - "FromFile", - title); - - tp.setSize(w,h); - - if(x>0 && y>0) - tp.setLocation(x,y); - - - Desktop.addInternalFrame(tp, title, w, h); - addTreeMenuItem(tp, title); - } - } - catch (Exception ex) - { - ex.printStackTrace(); - } - - return tp; - } - - class PrintThread - extends Thread - { - public void run() - { - PrinterJob printJob = PrinterJob.getPrinterJob(); - PageFormat pf = printJob.pageDialog(printJob.defaultPage()); - printJob.setPrintable(alignPanel, pf); - - if (printJob.printDialog()) - { - try - { - printJob.print(); - } - catch (Exception PrintException) - { - PrintException.printStackTrace(); - } - } - } - } - - /** - * Generates menu items and listener event actions for web service clients - * - */ - public void BuildWebServiceMenu() - { - if ( (Discoverer.services != null) - && (Discoverer.services.size() > 0)) - { - Vector msaws = (Vector) Discoverer.services.get("MsaWS"); - Vector secstrpr = (Vector) Discoverer.services.get("SecStrPred"); - Vector wsmenu = new Vector(); - if (msaws != null) - { - // Add any Multiple Sequence Alignment Services - final JMenu msawsmenu = new JMenu("Alignment"); - for (int i = 0, j = msaws.size(); i < j; i++) - { - final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle) msaws. - get(i); - final JMenuItem method = new JMenuItem(sh.getName()); - method.addActionListener(new ActionListener() - { - public void actionPerformed(ActionEvent e) - { - SequenceI[] msa = gatherSequencesForAlignment(); - new jalview.ws.MsaWSClient(sh, title, msa, - false, true); - - } - - }); - msawsmenu.add(method); - // Deal with services that we know accept partial alignments. - if (sh.getName().indexOf("lustal") > -1) - { - // We know that ClustalWS can accept partial alignments for refinement. - final JMenuItem methodR = new JMenuItem(sh.getName()+" Realign"); - methodR.addActionListener(new ActionListener() - { - public void actionPerformed(ActionEvent e) - { - SequenceI[] msa = gatherSequencesForAlignment(); - new jalview.ws.MsaWSClient(sh, title, msa, - true, true); - - } - - }); - msawsmenu.add(methodR); - - } - } - wsmenu.add(msawsmenu); - } - if (secstrpr != null) - { - // Add any secondary structure prediction services - final JMenu secstrmenu = new JMenu("Secondary Structure Prediction"); - for (int i = 0, j = secstrpr.size(); i < j; i++) - { - final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle) - secstrpr.get(i); - final JMenuItem method = new JMenuItem(sh.getName()); - method.addActionListener(new ActionListener() - { - public void actionPerformed(ActionEvent e) - { - SequenceI[] msa = gatherSeqOrMsaForSecStrPrediction(); - if (msa.length == 1) - { - // Single Sequence prediction - new jalview.ws.JPredClient(sh,title, msa[0]); - } - else - { - if (msa.length > 1) - { - // Single Sequence prediction - jalview.ws.JPredClient ct = new jalview.ws.JPredClient(sh, - title, msa); - } - } - } - }); - secstrmenu.add(method); - } - wsmenu.add(secstrmenu); - } - this.webService.removeAll(); - for (int i = 0, j = wsmenu.size(); i < j; i++) - { - webService.add( (JMenu) wsmenu.get(i)); - } - } - else - { - this.webService.removeAll(); - this.webService.add(this.webServiceNoServices); - } - // TODO: add in rediscovery function - // TODO: reduce code redundancy. - // TODO: group services by location as well as function. - } - - public void vamsasStore_actionPerformed(ActionEvent e) -{ - /* JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache. - getProperty("LAST_DIRECTORY")); - - chooser.setFileView(new JalviewFileView()); - chooser.setDialogTitle("Export to Vamsas file"); - chooser.setToolTipText("Export"); - - int value = chooser.showSaveDialog(this); - */ - // if (value == JalviewFileChooser.APPROVE_OPTION) - { - jalview.io.VamsasDatastore vs = new jalview.io.VamsasDatastore(viewport); - vs.store("C:\\Documents And Settings\\andrew\\Desktop\\vamsas.zip"); - // chooser.getSelectedFile().getAbsolutePath(); - } -} - -public void vamsasLoad_actionPerformed(ActionEvent e) -{ - jalview.io.VamsasDatastore vs = new jalview.io.VamsasDatastore(viewport); - vs.load("C:\\Documents And Settings\\andrew\\Desktop\\vamsas.zip"); -} - - -} +/* + * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$) + * Copyright (C) $$Year-Rel$$ The Jalview Authors + * + * This file is part of Jalview. + * + * Jalview is free software: you can redistribute it and/or + * modify it under the terms of the GNU General Public License + * as published by the Free Software Foundation, either version 3 + * of the License, or (at your option) any later version. + * + * Jalview is distributed in the hope that it will be useful, but + * WITHOUT ANY WARRANTY; without even the implied warranty + * of MERCHANTABILITY or FITNESS FOR A PARTICULAR + * PURPOSE. See the GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License + * along with Jalview. If not, see . + * The Jalview Authors are detailed in the 'AUTHORS' file. + */ +package jalview.gui; + +import jalview.analysis.AlignmentSorter; +import jalview.analysis.AlignmentUtils; +import jalview.analysis.CrossRef; +import jalview.analysis.Dna; +import jalview.analysis.ParseProperties; +import jalview.analysis.SequenceIdMatcher; +import jalview.api.AlignExportSettingI; +import jalview.api.AlignViewControllerGuiI; +import jalview.api.AlignViewControllerI; +import jalview.api.AlignViewportI; +import jalview.api.AlignmentViewPanel; +import jalview.api.FeatureSettingsControllerI; +import jalview.api.FeatureSettingsModelI; +import jalview.api.SplitContainerI; +import jalview.api.ViewStyleI; +import jalview.api.analysis.ScoreModelI; +import jalview.bin.Cache; +import jalview.bin.Jalview; +import jalview.commands.CommandI; +import jalview.commands.EditCommand; +import jalview.commands.EditCommand.Action; +import jalview.commands.OrderCommand; +import jalview.commands.RemoveGapColCommand; +import jalview.commands.RemoveGapsCommand; +import jalview.commands.SlideSequencesCommand; +import jalview.commands.TrimRegionCommand; +import jalview.datamodel.AlignedCodonFrame; +import jalview.datamodel.Alignment; +import jalview.datamodel.AlignmentAnnotation; +import jalview.datamodel.AlignmentExportData; +import jalview.datamodel.AlignmentI; +import jalview.datamodel.AlignmentOrder; +import jalview.datamodel.AlignmentView; +import jalview.datamodel.ColumnSelection; +import jalview.datamodel.DBRefSource; +import jalview.datamodel.HiddenSequences; +import jalview.datamodel.PDBEntry; +import jalview.datamodel.SeqCigar; +import jalview.datamodel.Sequence; +import jalview.datamodel.SequenceGroup; +import jalview.datamodel.SequenceI; +import jalview.gui.ViewSelectionMenu.ViewSetProvider; +import jalview.io.AlignmentProperties; +import jalview.io.AnnotationFile; +import jalview.io.BioJsHTMLOutput; +import jalview.io.FileLoader; +import jalview.io.FormatAdapter; +import jalview.io.HtmlSvgOutput; +import jalview.io.IdentifyFile; +import jalview.io.JalviewFileChooser; +import jalview.io.JalviewFileView; +import jalview.io.JnetAnnotationMaker; +import jalview.io.NewickFile; +import jalview.io.TCoffeeScoreFile; +import jalview.io.gff.SequenceOntologyI; +import jalview.jbgui.GAlignFrame; +import jalview.schemes.Blosum62ColourScheme; +import jalview.schemes.BuriedColourScheme; +import jalview.schemes.ClustalxColourScheme; +import jalview.schemes.ColourSchemeI; +import jalview.schemes.ColourSchemeProperty; +import jalview.schemes.HelixColourScheme; +import jalview.schemes.HydrophobicColourScheme; +import jalview.schemes.NucleotideColourScheme; +import jalview.schemes.PIDColourScheme; +import jalview.schemes.PurinePyrimidineColourScheme; +import jalview.schemes.RNAHelicesColourChooser; +import jalview.schemes.ResidueProperties; +import jalview.schemes.StrandColourScheme; +import jalview.schemes.TCoffeeColourScheme; +import jalview.schemes.TaylorColourScheme; +import jalview.schemes.TurnColourScheme; +import jalview.schemes.UserColourScheme; +import jalview.schemes.ZappoColourScheme; +import jalview.structure.StructureSelectionManager; +import jalview.util.MessageManager; +import jalview.viewmodel.AlignmentViewport; +import jalview.ws.DBRefFetcher; +import jalview.ws.DBRefFetcher.FetchFinishedListenerI; +import jalview.ws.SequenceFetcher; +import jalview.ws.jws1.Discoverer; +import jalview.ws.jws2.Jws2Discoverer; +import jalview.ws.jws2.jabaws2.Jws2Instance; +import jalview.ws.seqfetcher.DbSourceProxy; + +import java.awt.BorderLayout; +import java.awt.Component; +import java.awt.Rectangle; +import java.awt.Toolkit; +import java.awt.datatransfer.Clipboard; +import java.awt.datatransfer.DataFlavor; +import java.awt.datatransfer.StringSelection; +import java.awt.datatransfer.Transferable; +import java.awt.dnd.DropTargetDragEvent; +import java.awt.dnd.DropTargetDropEvent; +import java.awt.dnd.DropTargetEvent; +import java.awt.dnd.DropTargetListener; +import java.awt.event.ActionEvent; +import java.awt.event.ActionListener; +import java.awt.event.FocusAdapter; +import java.awt.event.FocusEvent; +import java.awt.event.ItemEvent; +import java.awt.event.ItemListener; +import java.awt.event.KeyAdapter; +import java.awt.event.KeyEvent; +import java.awt.event.MouseAdapter; +import java.awt.event.MouseEvent; +import java.awt.print.PageFormat; +import java.awt.print.PrinterJob; +import java.beans.PropertyChangeEvent; +import java.io.File; +import java.net.URL; +import java.util.ArrayList; +import java.util.Arrays; +import java.util.Deque; +import java.util.Enumeration; +import java.util.Hashtable; +import java.util.List; +import java.util.Vector; + +import javax.swing.JCheckBoxMenuItem; +import javax.swing.JEditorPane; +import javax.swing.JInternalFrame; +import javax.swing.JLayeredPane; +import javax.swing.JMenu; +import javax.swing.JMenuItem; +import javax.swing.JOptionPane; +import javax.swing.JRadioButtonMenuItem; +import javax.swing.JScrollPane; +import javax.swing.SwingUtilities; + +/** + * DOCUMENT ME! + * + * @author $author$ + * @version $Revision$ + */ +public class AlignFrame extends GAlignFrame implements DropTargetListener, + IProgressIndicator, AlignViewControllerGuiI +{ + + public static final int DEFAULT_WIDTH = 700; + + public static final int DEFAULT_HEIGHT = 500; + + /* + * The currently displayed panel (selected tabbed view if more than one) + */ + public AlignmentPanel alignPanel; + + AlignViewport viewport; + + public AlignViewControllerI avc; + + List alignPanels = new ArrayList(); + + /** + * Last format used to load or save alignments in this window + */ + String currentFileFormat = null; + + /** + * Current filename for this alignment + */ + String fileName = null; + + /** + * Creates a new AlignFrame object with specific width and height. + * + * @param al + * @param width + * @param height + */ + public AlignFrame(AlignmentI al, int width, int height) + { + this(al, null, width, height); + } + + /** + * Creates a new AlignFrame object with specific width, height and + * sequenceSetId + * + * @param al + * @param width + * @param height + * @param sequenceSetId + */ + public AlignFrame(AlignmentI al, int width, int height, + String sequenceSetId) + { + this(al, null, width, height, sequenceSetId); + } + + /** + * Creates a new AlignFrame object with specific width, height and + * sequenceSetId + * + * @param al + * @param width + * @param height + * @param sequenceSetId + * @param viewId + */ + public AlignFrame(AlignmentI al, int width, int height, + String sequenceSetId, String viewId) + { + this(al, null, width, height, sequenceSetId, viewId); + } + + /** + * new alignment window with hidden columns + * + * @param al + * AlignmentI + * @param hiddenColumns + * ColumnSelection or null + * @param width + * Width of alignment frame + * @param height + * height of frame. + */ + public AlignFrame(AlignmentI al, ColumnSelection hiddenColumns, + int width, int height) + { + this(al, hiddenColumns, width, height, null); + } + + /** + * Create alignment frame for al with hiddenColumns, a specific width and + * height, and specific sequenceId + * + * @param al + * @param hiddenColumns + * @param width + * @param height + * @param sequenceSetId + * (may be null) + */ + public AlignFrame(AlignmentI al, ColumnSelection hiddenColumns, + int width, int height, String sequenceSetId) + { + this(al, hiddenColumns, width, height, sequenceSetId, null); + } + + /** + * Create alignment frame for al with hiddenColumns, a specific width and + * height, and specific sequenceId + * + * @param al + * @param hiddenColumns + * @param width + * @param height + * @param sequenceSetId + * (may be null) + * @param viewId + * (may be null) + */ + public AlignFrame(AlignmentI al, ColumnSelection hiddenColumns, + int width, int height, String sequenceSetId, String viewId) + { + setSize(width, height); + + if (al.getDataset() == null) + { + al.setDataset(null); + } + + viewport = new AlignViewport(al, hiddenColumns, sequenceSetId, viewId); + + alignPanel = new AlignmentPanel(this, viewport); + + addAlignmentPanel(alignPanel, true); + init(); + } + + public AlignFrame(AlignmentI al, SequenceI[] hiddenSeqs, + ColumnSelection hiddenColumns, int width, int height) + { + setSize(width, height); + + if (al.getDataset() == null) + { + al.setDataset(null); + } + + viewport = new AlignViewport(al, hiddenColumns); + + if (hiddenSeqs != null && hiddenSeqs.length > 0) + { + viewport.hideSequence(hiddenSeqs); + } + alignPanel = new AlignmentPanel(this, viewport); + addAlignmentPanel(alignPanel, true); + init(); + } + + /** + * Make a new AlignFrame from existing alignmentPanels + * + * @param ap + * AlignmentPanel + * @param av + * AlignViewport + */ + public AlignFrame(AlignmentPanel ap) + { + viewport = ap.av; + alignPanel = ap; + addAlignmentPanel(ap, false); + init(); + } + + /** + * initalise the alignframe from the underlying viewport data and the + * configurations + */ + void init() + { + if (!Jalview.isHeadlessMode()) + { + progressBar = new ProgressBar(this.statusPanel, this.statusBar); + } + + avc = new jalview.controller.AlignViewController(this, viewport, + alignPanel); + if (viewport.getAlignmentConservationAnnotation() == null) + { + BLOSUM62Colour.setEnabled(false); + conservationMenuItem.setEnabled(false); + modifyConservation.setEnabled(false); + // PIDColour.setEnabled(false); + // abovePIDThreshold.setEnabled(false); + // modifyPID.setEnabled(false); + } + + String sortby = jalview.bin.Cache.getDefault("SORT_ALIGNMENT", + "No sort"); + + if (sortby.equals("Id")) + { + sortIDMenuItem_actionPerformed(null); + } + else if (sortby.equals("Pairwise Identity")) + { + sortPairwiseMenuItem_actionPerformed(null); + } + + if (Desktop.desktop != null) + { + this.setDropTarget(new java.awt.dnd.DropTarget(this, this)); + addServiceListeners(); + setGUINucleotide(viewport.getAlignment().isNucleotide()); + } + + this.alignPanel.av + .setShowAutocalculatedAbove(isShowAutoCalculatedAbove()); + + setMenusFromViewport(viewport); + buildSortByAnnotationScoresMenu(); + buildTreeMenu(); + + if (viewport.getWrapAlignment()) + { + wrapMenuItem_actionPerformed(null); + } + + if (jalview.bin.Cache.getDefault("SHOW_OVERVIEW", false)) + { + this.overviewMenuItem_actionPerformed(null); + } + + addKeyListener(); + + final List selviews = new ArrayList(); + final List origview = new ArrayList(); + final String menuLabel = MessageManager + .getString("label.copy_format_from"); + ViewSelectionMenu vsel = new ViewSelectionMenu(menuLabel, + new ViewSetProvider() + { + + @Override + public AlignmentPanel[] getAllAlignmentPanels() + { + origview.clear(); + origview.add(alignPanel); + // make an array of all alignment panels except for this one + List aps = new ArrayList( + Arrays.asList(Desktop.getAlignmentPanels(null))); + aps.remove(AlignFrame.this.alignPanel); + return aps.toArray(new AlignmentPanel[aps.size()]); + } + }, selviews, new ItemListener() + { + + @Override + public void itemStateChanged(ItemEvent e) + { + if (origview.size() > 0) + { + final AlignmentPanel ap = origview.get(0); + + /* + * Copy the ViewStyle of the selected panel to 'this one'. + * Don't change value of 'scaleProteinAsCdna' unless copying + * from a SplitFrame. + */ + ViewStyleI vs = selviews.get(0).getAlignViewport() + .getViewStyle(); + boolean fromSplitFrame = selviews.get(0) + .getAlignViewport().getCodingComplement() != null; + if (!fromSplitFrame) + { + vs.setScaleProteinAsCdna(ap.getAlignViewport() + .getViewStyle().isScaleProteinAsCdna()); + } + ap.getAlignViewport().setViewStyle(vs); + + /* + * Also rescale ViewStyle of SplitFrame complement if there is + * one _and_ it is set to 'scaledProteinAsCdna'; we don't copy + * the whole ViewStyle (allow cDNA protein to have different + * fonts) + */ + AlignViewportI complement = ap.getAlignViewport() + .getCodingComplement(); + if (complement != null && vs.isScaleProteinAsCdna()) + { + AlignFrame af = Desktop.getAlignFrameFor(complement); + ((SplitFrame) af.getSplitViewContainer()) + .adjustLayout(); + af.setMenusForViewport(); + } + + ap.updateLayout(); + ap.setSelected(true); + ap.alignFrame.setMenusForViewport(); + + } + } + }); + if (Cache.getDefault("VERSION", "DEVELOPMENT").toLowerCase() + .indexOf("devel") > -1 + || Cache.getDefault("VERSION", "DEVELOPMENT").toLowerCase() + .indexOf("test") > -1) + { + formatMenu.add(vsel); + } + addFocusListener(new FocusAdapter() + { + @Override + public void focusGained(FocusEvent e) + { + Jalview.setCurrentAlignFrame(AlignFrame.this); + } + }); + + } + + /** + * Change the filename and format for the alignment, and enable the 'reload' + * button functionality. + * + * @param file + * valid filename + * @param format + * format of file + */ + public void setFileName(String file, String format) + { + fileName = file; + setFileFormat(format); + reload.setEnabled(true); + } + + /** + * Add a KeyListener with handlers for various KeyPressed and KeyReleased + * events + */ + void addKeyListener() + { + addKeyListener(new KeyAdapter() + { + @Override + 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.getSeqPanel().numberPressed(evt.getKeyChar()); + } + + switch (evt.getKeyCode()) + { + + case 27: // escape key + deselectAllSequenceMenuItem_actionPerformed(null); + + break; + + case KeyEvent.VK_DOWN: + if (evt.isAltDown() || !viewport.cursorMode) + { + moveSelectedSequences(false); + } + if (viewport.cursorMode) + { + alignPanel.getSeqPanel().moveCursor(0, 1); + } + break; + + case KeyEvent.VK_UP: + if (evt.isAltDown() || !viewport.cursorMode) + { + moveSelectedSequences(true); + } + if (viewport.cursorMode) + { + alignPanel.getSeqPanel().moveCursor(0, -1); + } + + break; + + case KeyEvent.VK_LEFT: + if (evt.isAltDown() || !viewport.cursorMode) + { + slideSequences(false, alignPanel.getSeqPanel().getKeyboardNo1()); + } + else + { + alignPanel.getSeqPanel().moveCursor(-1, 0); + } + + break; + + case KeyEvent.VK_RIGHT: + if (evt.isAltDown() || !viewport.cursorMode) + { + slideSequences(true, alignPanel.getSeqPanel().getKeyboardNo1()); + } + else + { + alignPanel.getSeqPanel().moveCursor(1, 0); + } + break; + + case KeyEvent.VK_SPACE: + if (viewport.cursorMode) + { + alignPanel.getSeqPanel().insertGapAtCursor( + evt.isControlDown() || evt.isShiftDown() + || evt.isAltDown()); + } + break; + + // case KeyEvent.VK_A: + // if (viewport.cursorMode) + // { + // alignPanel.seqPanel.insertNucAtCursor(false,"A"); + // //System.out.println("A"); + // } + // break; + /* + * case KeyEvent.VK_CLOSE_BRACKET: if (viewport.cursorMode) { + * System.out.println("closing bracket"); } break; + */ + case KeyEvent.VK_DELETE: + case KeyEvent.VK_BACK_SPACE: + if (!viewport.cursorMode) + { + cut_actionPerformed(null); + } + else + { + alignPanel.getSeqPanel().deleteGapAtCursor( + evt.isControlDown() || evt.isShiftDown() + || evt.isAltDown()); + } + + break; + + case KeyEvent.VK_S: + if (viewport.cursorMode) + { + alignPanel.getSeqPanel().setCursorRow(); + } + break; + case KeyEvent.VK_C: + if (viewport.cursorMode && !evt.isControlDown()) + { + alignPanel.getSeqPanel().setCursorColumn(); + } + break; + case KeyEvent.VK_P: + if (viewport.cursorMode) + { + alignPanel.getSeqPanel().setCursorPosition(); + } + break; + + case KeyEvent.VK_ENTER: + case KeyEvent.VK_COMMA: + if (viewport.cursorMode) + { + alignPanel.getSeqPanel().setCursorRowAndColumn(); + } + break; + + case KeyEvent.VK_Q: + if (viewport.cursorMode) + { + alignPanel.getSeqPanel().setSelectionAreaAtCursor(true); + } + break; + case KeyEvent.VK_M: + if (viewport.cursorMode) + { + alignPanel.getSeqPanel().setSelectionAreaAtCursor(false); + } + break; + + case KeyEvent.VK_F2: + viewport.cursorMode = !viewport.cursorMode; + statusBar.setText(MessageManager.formatMessage( + "label.keyboard_editing_mode", + new String[] { (viewport.cursorMode ? "on" : "off") })); + if (viewport.cursorMode) + { + alignPanel.getSeqPanel().seqCanvas.cursorX = viewport.startRes; + alignPanel.getSeqPanel().seqCanvas.cursorY = viewport.startSeq; + } + alignPanel.getSeqPanel().seqCanvas.repaint(); + break; + + case KeyEvent.VK_F1: + try + { + Help.showHelpWindow(); + } catch (Exception ex) + { + ex.printStackTrace(); + } + break; + case KeyEvent.VK_H: + { + boolean toggleSeqs = !evt.isControlDown(); + boolean toggleCols = !evt.isShiftDown(); + toggleHiddenRegions(toggleSeqs, toggleCols); + break; + } + case KeyEvent.VK_PAGE_UP: + if (viewport.getWrapAlignment()) + { + alignPanel.scrollUp(true); + } + else + { + alignPanel.setScrollValues(viewport.startRes, viewport.startSeq + - viewport.endSeq + viewport.startSeq); + } + break; + case KeyEvent.VK_PAGE_DOWN: + if (viewport.getWrapAlignment()) + { + alignPanel.scrollUp(false); + } + else + { + alignPanel.setScrollValues(viewport.startRes, viewport.startSeq + + viewport.endSeq - viewport.startSeq); + } + break; + } + } + + @Override + public void keyReleased(KeyEvent evt) + { + switch (evt.getKeyCode()) + { + case KeyEvent.VK_LEFT: + if (evt.isAltDown() || !viewport.cursorMode) + { + viewport.firePropertyChange("alignment", null, viewport + .getAlignment().getSequences()); + } + break; + + case KeyEvent.VK_RIGHT: + if (evt.isAltDown() || !viewport.cursorMode) + { + viewport.firePropertyChange("alignment", null, viewport + .getAlignment().getSequences()); + } + break; + } + } + }); + } + + public void addAlignmentPanel(final AlignmentPanel ap, boolean newPanel) + { + ap.alignFrame = this; + avc = new jalview.controller.AlignViewController(this, viewport, + alignPanel); + + alignPanels.add(ap); + + PaintRefresher.Register(ap, ap.av.getSequenceSetId()); + + int aSize = alignPanels.size(); + + tabbedPane.setVisible(aSize > 1 || ap.av.viewName != null); + + if (aSize == 1 && ap.av.viewName == null) + { + this.getContentPane().add(ap, BorderLayout.CENTER); + } + else + { + if (aSize == 2) + { + setInitialTabVisible(); + } + + expandViews.setEnabled(true); + gatherViews.setEnabled(true); + tabbedPane.addTab(ap.av.viewName, ap); + + ap.setVisible(false); + } + + if (newPanel) + { + if (ap.av.isPadGaps()) + { + ap.av.getAlignment().padGaps(); + } + ap.av.updateConservation(ap); + ap.av.updateConsensus(ap); + ap.av.updateStrucConsensus(ap); + } + } + + public void setInitialTabVisible() + { + expandViews.setEnabled(true); + gatherViews.setEnabled(true); + tabbedPane.setVisible(true); + AlignmentPanel first = alignPanels.get(0); + tabbedPane.addTab(first.av.viewName, first); + this.getContentPane().add(tabbedPane, BorderLayout.CENTER); + } + + public AlignViewport getViewport() + { + return viewport; + } + + /* Set up intrinsic listeners for dynamically generated GUI bits. */ + private void addServiceListeners() + { + final java.beans.PropertyChangeListener thisListener; + Desktop.instance.addJalviewPropertyChangeListener("services", + thisListener = new java.beans.PropertyChangeListener() + { + @Override + public void propertyChange(PropertyChangeEvent evt) + { + // // System.out.println("Discoverer property change."); + // if (evt.getPropertyName().equals("services")) + { + SwingUtilities.invokeLater(new Runnable() + { + + @Override + public void run() + { + System.err + .println("Rebuild WS Menu for service change"); + BuildWebServiceMenu(); + } + + }); + } + } + }); + addInternalFrameListener(new javax.swing.event.InternalFrameAdapter() + { + @Override + public void internalFrameClosed( + javax.swing.event.InternalFrameEvent evt) + { + // System.out.println("deregistering discoverer listener"); + Desktop.instance.removeJalviewPropertyChangeListener("services", + thisListener); + closeMenuItem_actionPerformed(true); + }; + }); + // Finally, build the menu once to get current service state + new Thread(new Runnable() + { + @Override + public void run() + { + BuildWebServiceMenu(); + } + }).start(); + } + + /** + * Configure menu items that vary according to whether the alignment is + * nucleotide or protein + * + * @param nucleotide + */ + public void setGUINucleotide(boolean nucleotide) + { + showTranslation.setVisible(nucleotide); + showReverse.setVisible(nucleotide); + showReverseComplement.setVisible(nucleotide); + conservationMenuItem.setEnabled(!nucleotide); + modifyConservation.setEnabled(!nucleotide); + showGroupConservation.setEnabled(!nucleotide); + rnahelicesColour.setEnabled(nucleotide); + purinePyrimidineColour.setEnabled(nucleotide); + showComplementMenuItem.setText(MessageManager + .getString(nucleotide ? "label.protein" : "label.nucleotide")); + setColourSelected(jalview.bin.Cache.getDefault( + nucleotide ? Preferences.DEFAULT_COLOUR_NUC + : Preferences.DEFAULT_COLOUR_PROT, "None")); + } + + /** + * set up menus for the current viewport. This may be called after any + * operation that affects the data in the current view (selection changed, + * etc) to update the menus to reflect the new state. + */ + @Override + public void setMenusForViewport() + { + setMenusFromViewport(viewport); + } + + /** + * Need to call this method when tabs are selected for multiple views, or when + * loading from Jalview2XML.java + * + * @param av + * AlignViewport + */ + void setMenusFromViewport(AlignViewport av) + { + padGapsMenuitem.setSelected(av.isPadGaps()); + colourTextMenuItem.setSelected(av.isShowColourText()); + abovePIDThreshold.setSelected(av.getAbovePIDThreshold()); + conservationMenuItem.setSelected(av.getConservationSelected()); + seqLimits.setSelected(av.getShowJVSuffix()); + idRightAlign.setSelected(av.isRightAlignIds()); + centreColumnLabelsMenuItem.setState(av.isCentreColumnLabels()); + renderGapsMenuItem.setSelected(av.isRenderGaps()); + wrapMenuItem.setSelected(av.getWrapAlignment()); + scaleAbove.setVisible(av.getWrapAlignment()); + scaleLeft.setVisible(av.getWrapAlignment()); + scaleRight.setVisible(av.getWrapAlignment()); + annotationPanelMenuItem.setState(av.isShowAnnotation()); + /* + * Show/hide annotations only enabled if annotation panel is shown + */ + showAllSeqAnnotations.setEnabled(annotationPanelMenuItem.getState()); + hideAllSeqAnnotations.setEnabled(annotationPanelMenuItem.getState()); + showAllAlAnnotations.setEnabled(annotationPanelMenuItem.getState()); + hideAllAlAnnotations.setEnabled(annotationPanelMenuItem.getState()); + viewBoxesMenuItem.setSelected(av.getShowBoxes()); + viewTextMenuItem.setSelected(av.getShowText()); + showNonconservedMenuItem.setSelected(av.getShowUnconserved()); + showGroupConsensus.setSelected(av.isShowGroupConsensus()); + showGroupConservation.setSelected(av.isShowGroupConservation()); + showConsensusHistogram.setSelected(av.isShowConsensusHistogram()); + showSequenceLogo.setSelected(av.isShowSequenceLogo()); + normaliseSequenceLogo.setSelected(av.isNormaliseSequenceLogo()); + + setColourSelected(ColourSchemeProperty.getColourName(av + .getGlobalColourScheme())); + + showSeqFeatures.setSelected(av.isShowSequenceFeatures()); + hiddenMarkers.setState(av.getShowHiddenMarkers()); + applyToAllGroups.setState(av.getColourAppliesToAllGroups()); + showNpFeatsMenuitem.setSelected(av.isShowNPFeats()); + showDbRefsMenuitem.setSelected(av.isShowDBRefs()); + autoCalculate.setSelected(av.autoCalculateConsensus); + sortByTree.setSelected(av.sortByTree); + listenToViewSelections.setSelected(av.followSelection); + rnahelicesColour.setEnabled(av.getAlignment().hasRNAStructure()); + rnahelicesColour + .setSelected(av.getGlobalColourScheme() instanceof jalview.schemes.RNAHelicesColour); + + showProducts.setEnabled(canShowProducts()); + setGroovyEnabled(Desktop.getGroovyConsole() != null); + + updateEditMenuBar(); + } + + /** + * Set the enabled state of the 'Run Groovy' option in the Calculate menu + * + * @param b + */ + public void setGroovyEnabled(boolean b) + { + runGroovy.setEnabled(b); + } + + private IProgressIndicator progressBar; + + /* + * (non-Javadoc) + * + * @see jalview.gui.IProgressIndicator#setProgressBar(java.lang.String, long) + */ + @Override + public void setProgressBar(String message, long id) + { + progressBar.setProgressBar(message, id); + } + + @Override + public void registerHandler(final long id, + final IProgressIndicatorHandler handler) + { + progressBar.registerHandler(id, handler); + } + + /** + * + * @return true if any progress bars are still active + */ + @Override + public boolean operationInProgress() + { + return progressBar.operationInProgress(); + } + + @Override + public void setStatus(String text) + { + statusBar.setText(text); + } + + /* + * Added so Castor Mapping file can obtain Jalview Version + */ + public String getVersion() + { + return jalview.bin.Cache.getProperty("VERSION"); + } + + public FeatureRenderer getFeatureRenderer() + { + return alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer(); + } + + @Override + public void fetchSequence_actionPerformed(ActionEvent e) + { + new jalview.gui.SequenceFetcher(this); + } + + @Override + public void addFromFile_actionPerformed(ActionEvent e) + { + Desktop.instance.inputLocalFileMenuItem_actionPerformed(viewport); + } + + @Override + public void reload_actionPerformed(ActionEvent e) + { + if (fileName != null) + { + // TODO: JAL-1108 - ensure all associated frames are closed regardless of + // originating file's format + // TODO: work out how to recover feature settings for correct view(s) when + // file is reloaded. + if (currentFileFormat.equals("Jalview")) + { + JInternalFrame[] frames = Desktop.desktop.getAllFrames(); + for (int i = 0; i < frames.length; i++) + { + if (frames[i] instanceof AlignFrame && frames[i] != this + && ((AlignFrame) frames[i]).fileName != null + && ((AlignFrame) frames[i]).fileName.equals(fileName)) + { + try + { + frames[i].setSelected(true); + Desktop.instance.closeAssociatedWindows(); + } catch (java.beans.PropertyVetoException ex) + { + } + } + + } + Desktop.instance.closeAssociatedWindows(); + + FileLoader loader = new FileLoader(); + String protocol = fileName.startsWith("http:") ? "URL" : "File"; + loader.LoadFile(viewport, fileName, protocol, currentFileFormat); + } + else + { + Rectangle bounds = this.getBounds(); + + FileLoader loader = new FileLoader(); + String protocol = fileName.startsWith("http:") ? "URL" : "File"; + AlignFrame newframe = loader.LoadFileWaitTillLoaded(fileName, + protocol, currentFileFormat); + + newframe.setBounds(bounds); + if (featureSettings != null && featureSettings.isShowing()) + { + final Rectangle fspos = featureSettings.frame.getBounds(); + // TODO: need a 'show feature settings' function that takes bounds - + // need to refactor Desktop.addFrame + newframe.featureSettings_actionPerformed(null); + final FeatureSettings nfs = newframe.featureSettings; + SwingUtilities.invokeLater(new Runnable() + { + @Override + public void run() + { + nfs.frame.setBounds(fspos); + } + }); + this.featureSettings.close(); + this.featureSettings = null; + } + this.closeMenuItem_actionPerformed(true); + } + } + } + + @Override + public void addFromText_actionPerformed(ActionEvent e) + { + Desktop.instance.inputTextboxMenuItem_actionPerformed(viewport + .getAlignPanel()); + } + + @Override + public void addFromURL_actionPerformed(ActionEvent e) + { + Desktop.instance.inputURLMenuItem_actionPerformed(viewport); + } + + @Override + public void save_actionPerformed(ActionEvent e) + { + if (fileName == null + || (currentFileFormat == null || !jalview.io.FormatAdapter + .isValidIOFormat(currentFileFormat, true)) + || fileName.startsWith("http")) + { + saveAs_actionPerformed(null); + } + else + { + saveAlignment(fileName, currentFileFormat); + } + } + + /** + * DOCUMENT ME! + * + * @param e + * DOCUMENT ME! + */ + @Override + public void saveAs_actionPerformed(ActionEvent e) + { + JalviewFileChooser chooser = new JalviewFileChooser( + jalview.bin.Cache.getProperty("LAST_DIRECTORY"), + jalview.io.AppletFormatAdapter.WRITABLE_EXTENSIONS, + jalview.io.AppletFormatAdapter.WRITABLE_FNAMES, + currentFileFormat, false); + + chooser.setFileView(new JalviewFileView()); + chooser.setDialogTitle(MessageManager + .getString("label.save_alignment_to_file")); + chooser.setToolTipText(MessageManager.getString("action.save")); + + int value = chooser.showSaveDialog(this); + + if (value == JalviewFileChooser.APPROVE_OPTION) + { + currentFileFormat = chooser.getSelectedFormat(); + while (currentFileFormat == null) + { + JOptionPane + .showInternalMessageDialog( + Desktop.desktop, + MessageManager + .getString("label.select_file_format_before_saving"), + MessageManager + .getString("label.file_format_not_specified"), + JOptionPane.WARNING_MESSAGE); + currentFileFormat = chooser.getSelectedFormat(); + value = chooser.showSaveDialog(this); + if (value != JalviewFileChooser.APPROVE_OPTION) + { + return; + } + } + + fileName = chooser.getSelectedFile().getPath(); + + jalview.bin.Cache.setProperty("DEFAULT_FILE_FORMAT", + currentFileFormat); + + jalview.bin.Cache.setProperty("LAST_DIRECTORY", fileName); + if (currentFileFormat.indexOf(" ") > -1) + { + currentFileFormat = currentFileFormat.substring(0, + currentFileFormat.indexOf(" ")); + } + saveAlignment(fileName, currentFileFormat); + } + } + + public boolean saveAlignment(String file, String format) + { + boolean success = true; + + if (format.equalsIgnoreCase("Jalview")) + { + String shortName = title; + + if (shortName.indexOf(java.io.File.separatorChar) > -1) + { + shortName = shortName.substring(shortName + .lastIndexOf(java.io.File.separatorChar) + 1); + } + + success = new Jalview2XML().saveAlignment(this, file, shortName); + + statusBar.setText(MessageManager.formatMessage( + "label.successfully_saved_to_file_in_format", new Object[] { + fileName, format })); + + } + else + { + if (!jalview.io.AppletFormatAdapter.isValidFormat(format, true)) + { + warningMessage("Cannot save file " + fileName + " using format " + + format, "Alignment output format not supported"); + if (!Jalview.isHeadlessMode()) + { + saveAs_actionPerformed(null); + } + return false; + } + + AlignmentExportData exportData = getAlignmentForExport(format, + viewport, null); + if (exportData.getSettings().isCancelled()) + { + return false; + } + FormatAdapter f = new FormatAdapter(alignPanel, + exportData.getSettings()); + String output = f.formatSequences( + format, + exportData.getAlignment(), // class cast exceptions will + // occur in the distant future + exportData.getOmitHidden(), exportData.getStartEndPostions(), + f.getCacheSuffixDefault(format), + viewport.getColumnSelection()); + + if (output == null) + { + success = false; + } + else + { + try + { + java.io.PrintWriter out = new java.io.PrintWriter( + new java.io.FileWriter(file)); + + out.print(output); + out.close(); + this.setTitle(file); + statusBar.setText(MessageManager.formatMessage( + "label.successfully_saved_to_file_in_format", + new Object[] { fileName, format })); + } catch (Exception ex) + { + success = false; + ex.printStackTrace(); + } + } + } + + if (!success) + { + JOptionPane.showInternalMessageDialog(this, MessageManager + .formatMessage("label.couldnt_save_file", + new Object[] { fileName }), MessageManager + .getString("label.error_saving_file"), + JOptionPane.WARNING_MESSAGE); + } + + return success; + } + + private void warningMessage(String warning, String title) + { + if (new jalview.util.Platform().isHeadless()) + { + System.err.println("Warning: " + title + "\nWarning: " + warning); + + } + else + { + JOptionPane.showInternalMessageDialog(this, warning, title, + JOptionPane.WARNING_MESSAGE); + } + return; + } + + /** + * DOCUMENT ME! + * + * @param e + * DOCUMENT ME! + */ + @Override + protected void outputText_actionPerformed(ActionEvent e) + { + + AlignmentExportData exportData = getAlignmentForExport( + e.getActionCommand(), viewport, null); + if (exportData.getSettings().isCancelled()) + { + return; + } + CutAndPasteTransfer cap = new CutAndPasteTransfer(); + cap.setForInput(null); + try + { + cap.setText(new FormatAdapter(alignPanel, exportData.getSettings()) + .formatSequences(e.getActionCommand(), + exportData.getAlignment(), + exportData.getOmitHidden(), + exportData.getStartEndPostions(), + viewport.getColumnSelection())); + Desktop.addInternalFrame(cap, MessageManager.formatMessage( + "label.alignment_output_command", + new Object[] { e.getActionCommand() }), 600, 500); + } catch (OutOfMemoryError oom) + { + new OOMWarning("Outputting alignment as " + e.getActionCommand(), oom); + cap.dispose(); + } + + } + + public static AlignmentExportData getAlignmentForExport( + String exportFormat, AlignViewportI viewport, + AlignExportSettingI exportSettings) + { + AlignmentI alignmentToExport = null; + AlignExportSettingI settings = exportSettings; + String[] omitHidden = null; + + HiddenSequences hiddenSeqs = viewport.getAlignment() + .getHiddenSequences(); + + alignmentToExport = viewport.getAlignment(); + + boolean hasHiddenSeqs = hiddenSeqs.getSize() > 0; + if (settings == null) + { + settings = new AlignExportSettings(hasHiddenSeqs, + viewport.hasHiddenColumns(), exportFormat); + } + // settings.isExportAnnotations(); + + if (viewport.hasHiddenColumns() && !settings.isExportHiddenColumns()) + { + omitHidden = viewport.getViewAsString(false, + settings.isExportHiddenSequences()); + } + + int[] alignmentStartEnd = new int[2]; + if (hasHiddenSeqs && settings.isExportHiddenSequences()) + { + alignmentToExport = hiddenSeqs.getFullAlignment(); + } + else + { + alignmentToExport = viewport.getAlignment(); + } + alignmentStartEnd = alignmentToExport + .getVisibleStartAndEndIndex(viewport.getColumnSelection() + .getHiddenColumns()); + AlignmentExportData ed = new AlignmentExportData(alignmentToExport, + omitHidden, alignmentStartEnd, settings); + return ed; + } + + /** + * DOCUMENT ME! + * + * @param e + * DOCUMENT ME! + */ + @Override + protected void htmlMenuItem_actionPerformed(ActionEvent e) + { + new HtmlSvgOutput(null, alignPanel); + } + + @Override + public void bioJSMenuItem_actionPerformed(ActionEvent e) + { + BioJsHTMLOutput bjs = new BioJsHTMLOutput(alignPanel, this); + bjs.exportJalviewAlignmentAsBioJsHtmlFile(); + } + + public void createImageMap(File file, String image) + { + alignPanel.makePNGImageMap(file, image); + } + + /** + * DOCUMENT ME! + * + * @param e + * DOCUMENT ME! + */ + @Override + public void createPNG(File f) + { + alignPanel.makePNG(f); + } + + /** + * DOCUMENT ME! + * + * @param e + * DOCUMENT ME! + */ + @Override + public void createEPS(File f) + { + alignPanel.makeEPS(f); + } + + @Override + public void createSVG(File f) + { + alignPanel.makeSVG(f); + } + + @Override + public void pageSetup_actionPerformed(ActionEvent e) + { + PrinterJob printJob = PrinterJob.getPrinterJob(); + PrintThread.pf = printJob.pageDialog(printJob.defaultPage()); + } + + /** + * DOCUMENT ME! + * + * @param e + * DOCUMENT ME! + */ + @Override + public void printMenuItem_actionPerformed(ActionEvent e) + { + // Putting in a thread avoids Swing painting problems + PrintThread thread = new PrintThread(alignPanel); + thread.start(); + } + + @Override + public void exportFeatures_actionPerformed(ActionEvent e) + { + new AnnotationExporter().exportFeatures(alignPanel); + } + + @Override + public void exportAnnotations_actionPerformed(ActionEvent e) + { + new AnnotationExporter().exportAnnotations(alignPanel); + } + + @Override + public void associatedData_actionPerformed(ActionEvent e) + { + // Pick the tree file + JalviewFileChooser chooser = new JalviewFileChooser( + jalview.bin.Cache.getProperty("LAST_DIRECTORY")); + chooser.setFileView(new JalviewFileView()); + chooser.setDialogTitle(MessageManager + .getString("label.load_jalview_annotations")); + chooser.setToolTipText(MessageManager + .getString("label.load_jalview_annotations")); + + int value = chooser.showOpenDialog(null); + + if (value == JalviewFileChooser.APPROVE_OPTION) + { + String choice = chooser.getSelectedFile().getPath(); + jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice); + loadJalviewDataFile(choice, null, null, null); + } + + } + + /** + * Close the current view or all views in the alignment frame. If the frame + * only contains one view then the alignment will be removed from memory. + * + * @param closeAllTabs + */ + @Override + public void closeMenuItem_actionPerformed(boolean closeAllTabs) + { + if (alignPanels != null && alignPanels.size() < 2) + { + closeAllTabs = true; + } + + try + { + if (alignPanels != null) + { + if (closeAllTabs) + { + if (this.isClosed()) + { + // really close all the windows - otherwise wait till + // setClosed(true) is called + for (int i = 0; i < alignPanels.size(); i++) + { + AlignmentPanel ap = alignPanels.get(i); + ap.closePanel(); + } + } + } + else + { + closeView(alignPanel); + } + } + + if (closeAllTabs) + { + /* + * this will raise an INTERNAL_FRAME_CLOSED event and this method will + * be called recursively, with the frame now in 'closed' state + */ + this.setClosed(true); + } + } catch (Exception ex) + { + ex.printStackTrace(); + } + } + + /** + * Close the specified panel and close up tabs appropriately. + * + * @param panelToClose + */ + public void closeView(AlignmentPanel panelToClose) + { + int index = tabbedPane.getSelectedIndex(); + int closedindex = tabbedPane.indexOfComponent(panelToClose); + alignPanels.remove(panelToClose); + panelToClose.closePanel(); + panelToClose = null; + + tabbedPane.removeTabAt(closedindex); + tabbedPane.validate(); + + if (index > closedindex || index == tabbedPane.getTabCount()) + { + // modify currently selected tab index if necessary. + index--; + } + + this.tabSelectionChanged(index); + } + + /** + * DOCUMENT ME! + */ + void updateEditMenuBar() + { + + if (viewport.getHistoryList().size() > 0) + { + undoMenuItem.setEnabled(true); + CommandI command = viewport.getHistoryList().peek(); + undoMenuItem.setText(MessageManager.formatMessage( + "label.undo_command", + new Object[] { command.getDescription() })); + } + else + { + undoMenuItem.setEnabled(false); + undoMenuItem.setText(MessageManager.getString("action.undo")); + } + + if (viewport.getRedoList().size() > 0) + { + redoMenuItem.setEnabled(true); + + CommandI command = viewport.getRedoList().peek(); + redoMenuItem.setText(MessageManager.formatMessage( + "label.redo_command", + new Object[] { command.getDescription() })); + } + else + { + redoMenuItem.setEnabled(false); + redoMenuItem.setText(MessageManager.getString("action.redo")); + } + } + + @Override + public void addHistoryItem(CommandI command) + { + if (command.getSize() > 0) + { + viewport.addToHistoryList(command); + viewport.clearRedoList(); + updateEditMenuBar(); + viewport.updateHiddenColumns(); + // viewport.hasHiddenColumns = (viewport.getColumnSelection() != null + // && viewport.getColumnSelection().getHiddenColumns() != null && + // viewport.getColumnSelection() + // .getHiddenColumns().size() > 0); + } + } + + /** + * + * @return alignment objects for all views + */ + AlignmentI[] getViewAlignments() + { + if (alignPanels != null) + { + AlignmentI[] als = new AlignmentI[alignPanels.size()]; + int i = 0; + for (AlignmentPanel ap : alignPanels) + { + als[i++] = ap.av.getAlignment(); + } + return als; + } + if (viewport != null) + { + return new AlignmentI[] { viewport.getAlignment() }; + } + return null; + } + + /** + * DOCUMENT ME! + * + * @param e + * DOCUMENT ME! + */ + @Override + protected void undoMenuItem_actionPerformed(ActionEvent e) + { + if (viewport.getHistoryList().isEmpty()) + { + return; + } + CommandI command = viewport.getHistoryList().pop(); + viewport.addToRedoList(command); + command.undoCommand(getViewAlignments()); + + AlignmentViewport originalSource = getOriginatingSource(command); + updateEditMenuBar(); + + if (originalSource != null) + { + if (originalSource != viewport) + { + Cache.log + .warn("Implementation worry: mismatch of viewport origin for undo"); + } + originalSource.updateHiddenColumns(); + // originalSource.hasHiddenColumns = (viewport.getColumnSelection() != + // null + // && viewport.getColumnSelection().getHiddenColumns() != null && + // viewport.getColumnSelection() + // .getHiddenColumns().size() > 0); + originalSource.firePropertyChange("alignment", null, originalSource + .getAlignment().getSequences()); + } + } + + /** + * DOCUMENT ME! + * + * @param e + * DOCUMENT ME! + */ + @Override + protected void redoMenuItem_actionPerformed(ActionEvent e) + { + if (viewport.getRedoList().size() < 1) + { + return; + } + + CommandI command = viewport.getRedoList().pop(); + viewport.addToHistoryList(command); + command.doCommand(getViewAlignments()); + + AlignmentViewport originalSource = getOriginatingSource(command); + updateEditMenuBar(); + + if (originalSource != null) + { + + if (originalSource != viewport) + { + Cache.log + .warn("Implementation worry: mismatch of viewport origin for redo"); + } + originalSource.updateHiddenColumns(); + // originalSource.hasHiddenColumns = (viewport.getColumnSelection() != + // null + // && viewport.getColumnSelection().getHiddenColumns() != null && + // viewport.getColumnSelection() + // .getHiddenColumns().size() > 0); + originalSource.firePropertyChange("alignment", null, originalSource + .getAlignment().getSequences()); + } + } + + AlignmentViewport getOriginatingSource(CommandI command) + { + AlignmentViewport 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(); + List comps = PaintRefresher.components.get(viewport + .getSequenceSetId()); + + for (Component comp : comps) + { + if (comp instanceof AlignmentPanel) + { + if (al == ((AlignmentPanel) comp).av.getAlignment()) + { + originalSource = ((AlignmentPanel) comp).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.getAlignment()); + } + + originalSource = viewport; + } + + return originalSource; + } + + /** + * DOCUMENT ME! + * + * @param up + * DOCUMENT ME! + */ + public void moveSelectedSequences(boolean up) + { + SequenceGroup sg = viewport.getSelectionGroup(); + + if (sg == null) + { + return; + } + viewport.getAlignment().moveSelectedSequencesByOne(sg, + viewport.getHiddenRepSequences(), up); + alignPanel.paintAlignment(true); + } + + synchronized void slideSequences(boolean right, int size) + { + List sg = new ArrayList(); + if (viewport.cursorMode) + { + sg.add(viewport.getAlignment().getSequenceAt( + alignPanel.getSeqPanel().seqCanvas.cursorY)); + } + else if (viewport.getSelectionGroup() != null + && viewport.getSelectionGroup().getSize() != viewport + .getAlignment().getHeight()) + { + sg = viewport.getSelectionGroup().getSequences( + viewport.getHiddenRepSequences()); + } + + if (sg.size() < 1) + { + return; + } + + List invertGroup = new ArrayList(); + + for (SequenceI seq : viewport.getAlignment().getSequences()) + { + if (!sg.contains(seq)) + { + invertGroup.add(seq); + } + } + + SequenceI[] seqs1 = sg.toArray(new SequenceI[0]); + + SequenceI[] seqs2 = new SequenceI[invertGroup.size()]; + for (int i = 0; i < invertGroup.size(); i++) + { + seqs2[i] = invertGroup.get(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.getSeqPanel().moveCursor(size, 0); + } + else + { + groupAdjustment = size; + } + } + else if (!ssc.getGapsInsertedBegin() && !right) + { + if (viewport.cursorMode) + { + alignPanel.getSeqPanel().moveCursor(-size, 0); + } + else + { + groupAdjustment = -size; + } + } + + if (groupAdjustment != 0) + { + viewport.getSelectionGroup().setStartRes( + viewport.getSelectionGroup().getStartRes() + groupAdjustment); + viewport.getSelectionGroup().setEndRes( + viewport.getSelectionGroup().getEndRes() + groupAdjustment); + } + + /* + * just extend the last slide command if compatible; but not if in + * SplitFrame mode (to ensure all edits are broadcast - JAL-1802) + */ + boolean appendHistoryItem = false; + Deque historyList = viewport.getHistoryList(); + boolean inSplitFrame = getSplitViewContainer() != null; + if (!inSplitFrame && historyList != null && historyList.size() > 0 + && historyList.peek() instanceof SlideSequencesCommand) + { + appendHistoryItem = ssc + .appendSlideCommand((SlideSequencesCommand) historyList + .peek()); + } + + if (!appendHistoryItem) + { + addHistoryItem(ssc); + } + + repaint(); + } + + /** + * DOCUMENT ME! + * + * @param e + * DOCUMENT ME! + */ + @Override + protected void copy_actionPerformed(ActionEvent e) + { + System.gc(); + if (viewport.getSelectionGroup() == null) + { + return; + } + // TODO: preserve the ordering of displayed alignment annotation in any + // internal paste (particularly sequence associated annotation) + SequenceI[] seqs = viewport.getSelectionAsNewSequence(); + String[] omitHidden = null; + + if (viewport.hasHiddenColumns()) + { + omitHidden = viewport.getViewAsString(true); + } + + String output = new FormatAdapter().formatSequences("Fasta", seqs, + omitHidden, null); + + StringSelection ss = new StringSelection(output); + + try + { + jalview.gui.Desktop.internalCopy = true; + // Its really worth setting the clipboard contents + // to empty before setting the large StringSelection!! + Toolkit.getDefaultToolkit().getSystemClipboard() + .setContents(new StringSelection(""), null); + + Toolkit.getDefaultToolkit().getSystemClipboard() + .setContents(ss, Desktop.instance); + } catch (OutOfMemoryError er) + { + new OOMWarning("copying region", er); + return; + } + + ArrayList hiddenColumns = null; + if (viewport.hasHiddenColumns()) + { + hiddenColumns = new ArrayList(); + int hiddenOffset = viewport.getSelectionGroup().getStartRes(), hiddenCutoff = viewport + .getSelectionGroup().getEndRes(); + for (int[] region : viewport.getColumnSelection().getHiddenColumns()) + { + if (region[0] >= hiddenOffset && region[1] <= hiddenCutoff) + { + hiddenColumns.add(new int[] { region[0] - hiddenOffset, + region[1] - hiddenOffset }); + } + } + } + + Desktop.jalviewClipboard = new Object[] { seqs, + viewport.getAlignment().getDataset(), hiddenColumns }; + statusBar.setText(MessageManager.formatMessage( + "label.copied_sequences_to_clipboard", new Object[] { Integer + .valueOf(seqs.length).toString() })); + } + + /** + * DOCUMENT ME! + * + * @param e + * DOCUMENT ME! + */ + @Override + protected void pasteNew_actionPerformed(ActionEvent e) + { + paste(true); + } + + /** + * DOCUMENT ME! + * + * @param e + * DOCUMENT ME! + */ + @Override + protected void pasteThis_actionPerformed(ActionEvent e) + { + paste(false); + } + + /** + * Paste contents of Jalview clipboard + * + * @param newAlignment + * true to paste to a new alignment, otherwise add to this. + */ + void paste(boolean newAlignment) + { + boolean externalPaste = true; + try + { + Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard(); + Transferable contents = c.getContents(this); + + if (contents == null) + { + return; + } + + String str, format; + try + { + str = (String) contents.getTransferData(DataFlavor.stringFlavor); + if (str.length() < 1) + { + return; + } + + format = new IdentifyFile().identify(str, "Paste"); + + } catch (OutOfMemoryError er) + { + new OOMWarning("Out of memory pasting sequences!!", er); + return; + } + + SequenceI[] sequences; + boolean annotationAdded = false; + AlignmentI alignment = null; + + if (Desktop.jalviewClipboard != null) + { + // The clipboard was filled from within Jalview, we must use the + // sequences + // And dataset from the copied alignment + SequenceI[] newseq = (SequenceI[]) Desktop.jalviewClipboard[0]; + // be doubly sure that we create *new* sequence objects. + sequences = new SequenceI[newseq.length]; + for (int i = 0; i < newseq.length; i++) + { + sequences[i] = new Sequence(newseq[i]); + } + alignment = new Alignment(sequences); + externalPaste = false; + } + else + { + // parse the clipboard as an alignment. + alignment = new FormatAdapter().readFile(str, "Paste", format); + sequences = alignment.getSequencesArray(); + } + + int alwidth = 0; + ArrayList newGraphGroups = new ArrayList(); + int fgroup = -1; + + if (newAlignment) + { + + if (Desktop.jalviewClipboard != null) + { + // dataset is inherited + alignment.setDataset((Alignment) Desktop.jalviewClipboard[1]); + } + else + { + // new dataset is constructed + alignment.setDataset(null); + } + alwidth = alignment.getWidth() + 1; + } + else + { + AlignmentI pastedal = alignment; // preserve pasted alignment object + // Add pasted sequences and dataset into existing alignment. + alignment = viewport.getAlignment(); + alwidth = alignment.getWidth() + 1; + // decide if we need to import sequences from an existing dataset + boolean importDs = Desktop.jalviewClipboard != null + && Desktop.jalviewClipboard[1] != alignment.getDataset(); + // importDs==true instructs us to copy over new dataset sequences from + // an existing alignment + Vector newDs = (importDs) ? new Vector() : null; // used to create + // minimum dataset set + + for (int i = 0; i < sequences.length; i++) + { + if (importDs) + { + newDs.addElement(null); + } + SequenceI ds = sequences[i].getDatasetSequence(); // null for a simple + // paste + if (importDs && ds != null) + { + if (!newDs.contains(ds)) + { + newDs.setElementAt(ds, i); + ds = new Sequence(ds); + // update with new dataset sequence + sequences[i].setDatasetSequence(ds); + } + else + { + ds = sequences[newDs.indexOf(ds)].getDatasetSequence(); + } + } + else + { + // copy and derive new dataset sequence + sequences[i] = sequences[i].deriveSequence(); + alignment.getDataset().addSequence( + sequences[i].getDatasetSequence()); + // TODO: avoid creation of duplicate dataset sequences with a + // 'contains' method using SequenceI.equals()/SequenceI.contains() + } + alignment.addSequence(sequences[i]); // merges dataset + } + if (newDs != null) + { + newDs.clear(); // tidy up + } + if (alignment.getAlignmentAnnotation() != null) + { + for (AlignmentAnnotation alan : alignment + .getAlignmentAnnotation()) + { + if (alan.graphGroup > fgroup) + { + fgroup = alan.graphGroup; + } + } + } + if (pastedal.getAlignmentAnnotation() != null) + { + // Add any annotation attached to alignment. + AlignmentAnnotation[] alann = pastedal.getAlignmentAnnotation(); + for (int i = 0; i < alann.length; i++) + { + annotationAdded = true; + if (alann[i].sequenceRef == null && !alann[i].autoCalculated) + { + AlignmentAnnotation newann = new AlignmentAnnotation(alann[i]); + if (newann.graphGroup > -1) + { + if (newGraphGroups.size() <= newann.graphGroup + || newGraphGroups.get(newann.graphGroup) == null) + { + for (int q = newGraphGroups.size(); q <= newann.graphGroup; q++) + { + newGraphGroups.add(q, null); + } + newGraphGroups.set(newann.graphGroup, new Integer( + ++fgroup)); + } + newann.graphGroup = newGraphGroups.get(newann.graphGroup) + .intValue(); + } + + newann.padAnnotation(alwidth); + alignment.addAnnotation(newann); + } + } + } + } + if (!newAlignment) + { + // ///// + // ADD HISTORY ITEM + // + addHistoryItem(new EditCommand( + MessageManager.getString("label.add_sequences"), + Action.PASTE, sequences, 0, alignment.getWidth(), alignment)); + } + // Add any annotations attached to sequences + for (int i = 0; i < sequences.length; i++) + { + if (sequences[i].getAnnotation() != null) + { + AlignmentAnnotation newann; + for (int a = 0; a < sequences[i].getAnnotation().length; a++) + { + annotationAdded = true; + newann = sequences[i].getAnnotation()[a]; + newann.adjustForAlignment(); + newann.padAnnotation(alwidth); + if (newann.graphGroup > -1) + { + if (newann.graphGroup > -1) + { + if (newGraphGroups.size() <= newann.graphGroup + || newGraphGroups.get(newann.graphGroup) == null) + { + for (int q = newGraphGroups.size(); q <= newann.graphGroup; q++) + { + newGraphGroups.add(q, null); + } + newGraphGroups.set(newann.graphGroup, new Integer( + ++fgroup)); + } + newann.graphGroup = newGraphGroups.get(newann.graphGroup) + .intValue(); + } + } + alignment.addAnnotation(sequences[i].getAnnotation()[a]); // annotation + // was + // duplicated + // earlier + alignment + .setAnnotationIndex(sequences[i].getAnnotation()[a], a); + } + } + } + if (!newAlignment) + { + + // propagate alignment changed. + viewport.setEndSeq(alignment.getHeight()); + if (annotationAdded) + { + // Duplicate sequence annotation in all views. + AlignmentI[] alview = this.getViewAlignments(); + for (int i = 0; i < sequences.length; i++) + { + AlignmentAnnotation sann[] = sequences[i].getAnnotation(); + if (sann == null) + { + continue; + } + for (int avnum = 0; avnum < alview.length; avnum++) + { + if (alview[avnum] != alignment) + { + // duplicate in a view other than the one with input focus + int avwidth = alview[avnum].getWidth() + 1; + // this relies on sann being preserved after we + // modify the sequence's annotation array for each duplication + for (int a = 0; a < sann.length; a++) + { + AlignmentAnnotation newann = new AlignmentAnnotation( + sann[a]); + sequences[i].addAlignmentAnnotation(newann); + newann.padAnnotation(avwidth); + alview[avnum].addAnnotation(newann); // annotation was + // duplicated earlier + // TODO JAL-1145 graphGroups are not updated for sequence + // annotation added to several views. This may cause + // strangeness + alview[avnum].setAnnotationIndex(newann, a); + } + } + } + } + buildSortByAnnotationScoresMenu(); + } + viewport.firePropertyChange("alignment", null, + alignment.getSequences()); + if (alignPanels != null) + { + for (AlignmentPanel ap : alignPanels) + { + ap.validateAnnotationDimensions(false); + } + } + else + { + alignPanel.validateAnnotationDimensions(false); + } + + } + else + { + AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH, + DEFAULT_HEIGHT); + String newtitle = new String("Copied sequences"); + + if (Desktop.jalviewClipboard != null + && Desktop.jalviewClipboard[2] != null) + { + List hc = (List) Desktop.jalviewClipboard[2]; + for (int[] region : hc) + { + af.viewport.hideColumns(region[0], region[1]); + } + } + + // >>>This is a fix for the moment, until a better solution is + // found!!<<< + af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer() + .transferSettings( + alignPanel.getSeqPanel().seqCanvas + .getFeatureRenderer()); + + // TODO: maintain provenance of an alignment, rather than just make the + // title a concatenation of operations. + if (!externalPaste) + { + if (title.startsWith("Copied sequences")) + { + newtitle = title; + } + else + { + newtitle = newtitle.concat("- from " + title); + } + } + else + { + newtitle = new String("Pasted sequences"); + } + + Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH, + DEFAULT_HEIGHT); + + } + + } catch (Exception ex) + { + ex.printStackTrace(); + System.out.println("Exception whilst pasting: " + ex); + // could be anything being pasted in here + } + + } + + @Override + protected void expand_newalign(ActionEvent e) + { + try + { + AlignmentI alignment = AlignmentUtils.expandContext(getViewport() + .getAlignment(), -1); + AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH, + DEFAULT_HEIGHT); + String newtitle = new String("Flanking alignment"); + + if (Desktop.jalviewClipboard != null + && Desktop.jalviewClipboard[2] != null) + { + List hc = (List) Desktop.jalviewClipboard[2]; + for (int region[] : hc) + { + af.viewport.hideColumns(region[0], region[1]); + } + } + + // >>>This is a fix for the moment, until a better solution is + // found!!<<< + af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer() + .transferSettings( + alignPanel.getSeqPanel().seqCanvas + .getFeatureRenderer()); + + // TODO: maintain provenance of an alignment, rather than just make the + // title a concatenation of operations. + { + if (title.startsWith("Copied sequences")) + { + newtitle = title; + } + else + { + newtitle = newtitle.concat("- from " + title); + } + } + + Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH, DEFAULT_HEIGHT); + + } catch (Exception ex) + { + ex.printStackTrace(); + System.out.println("Exception whilst pasting: " + ex); + // could be anything being pasted in here + } catch (OutOfMemoryError oom) + { + new OOMWarning("Viewing flanking region of alignment", oom); + } + } + + /** + * DOCUMENT ME! + * + * @param e + * DOCUMENT ME! + */ + @Override + protected void cut_actionPerformed(ActionEvent e) + { + copy_actionPerformed(null); + delete_actionPerformed(null); + } + + /** + * DOCUMENT ME! + * + * @param e + * DOCUMENT ME! + */ + @Override + protected void delete_actionPerformed(ActionEvent evt) + { + + SequenceGroup sg = viewport.getSelectionGroup(); + if (sg == null) + { + return; + } + + /* + * If the cut affects all sequences, warn, remove highlighted columns + */ + if (sg.getSize() == viewport.getAlignment().getHeight()) + { + boolean isEntireAlignWidth = (((sg.getEndRes() - sg.getStartRes()) + 1) == viewport + .getAlignment().getWidth()) ? true : false; + if (isEntireAlignWidth) + { + int confirm = JOptionPane.showConfirmDialog(this, + MessageManager.getString("warn.delete_all"), // $NON-NLS-1$ + MessageManager.getString("label.delete_all"), // $NON-NLS-1$ + JOptionPane.OK_CANCEL_OPTION); + + if (confirm == JOptionPane.CANCEL_OPTION + || confirm == JOptionPane.CLOSED_OPTION) + { + return; + } + } + viewport.getColumnSelection().removeElements(sg.getStartRes(), + sg.getEndRes() + 1); + } + SequenceI[] cut = sg.getSequences() + .toArray(new SequenceI[sg.getSize()]); + + addHistoryItem(new EditCommand( + MessageManager.getString("label.cut_sequences"), Action.CUT, + cut, sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1, + viewport.getAlignment())); + + viewport.setSelectionGroup(null); + viewport.sendSelection(); + viewport.getAlignment().deleteGroup(sg); + + viewport.firePropertyChange("alignment", null, viewport.getAlignment() + .getSequences()); + if (viewport.getAlignment().getHeight() < 1) + { + try + { + this.setClosed(true); + } catch (Exception ex) + { + } + } + } + + /** + * DOCUMENT ME! + * + * @param e + * DOCUMENT ME! + */ + @Override + protected void deleteGroups_actionPerformed(ActionEvent e) + { + if (avc.deleteGroups()) + { + PaintRefresher.Refresh(this, viewport.getSequenceSetId()); + alignPanel.updateAnnotation(); + alignPanel.paintAlignment(true); + } + } + + /** + * DOCUMENT ME! + * + * @param e + * DOCUMENT ME! + */ + @Override + 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.getAlignment().getWidth() - 1); + viewport.setSelectionGroup(sg); + viewport.sendSelection(); + alignPanel.paintAlignment(true); + PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId()); + } + + /** + * DOCUMENT ME! + * + * @param e + * DOCUMENT ME! + */ + @Override + public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e) + { + if (viewport.cursorMode) + { + alignPanel.getSeqPanel().keyboardNo1 = null; + alignPanel.getSeqPanel().keyboardNo2 = null; + } + viewport.setSelectionGroup(null); + viewport.getColumnSelection().clear(); + viewport.setSelectionGroup(null); + alignPanel.getSeqPanel().seqCanvas.highlightSearchResults(null); + alignPanel.getIdPanel().getIdCanvas().searchResults = null; + alignPanel.paintAlignment(true); + PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId()); + viewport.sendSelection(); + } + + /** + * DOCUMENT ME! + * + * @param e + * DOCUMENT ME! + */ + @Override + public void invertSequenceMenuItem_actionPerformed(ActionEvent e) + { + SequenceGroup sg = viewport.getSelectionGroup(); + + if (sg == null) + { + selectAllSequenceMenuItem_actionPerformed(null); + + return; + } + + for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++) + { + sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false); + } + + alignPanel.paintAlignment(true); + PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId()); + viewport.sendSelection(); + } + + @Override + public void invertColSel_actionPerformed(ActionEvent e) + { + viewport.invertColumnSelection(); + alignPanel.paintAlignment(true); + viewport.sendSelection(); + } + + /** + * DOCUMENT ME! + * + * @param e + * DOCUMENT ME! + */ + @Override + public void remove2LeftMenuItem_actionPerformed(ActionEvent e) + { + trimAlignment(true); + } + + /** + * DOCUMENT ME! + * + * @param e + * DOCUMENT ME! + */ + @Override + public void remove2RightMenuItem_actionPerformed(ActionEvent e) + { + trimAlignment(false); + } + + void trimAlignment(boolean trimLeft) + { + ColumnSelection colSel = viewport.getColumnSelection(); + int column; + + if (!colSel.isEmpty()) + { + if (trimLeft) + { + column = colSel.getMin(); + } + else + { + column = colSel.getMax(); + } + + SequenceI[] seqs; + if (viewport.getSelectionGroup() != null) + { + seqs = viewport.getSelectionGroup().getSequencesAsArray( + viewport.getHiddenRepSequences()); + } + else + { + seqs = viewport.getAlignment().getSequencesArray(); + } + + TrimRegionCommand trimRegion; + if (trimLeft) + { + trimRegion = new TrimRegionCommand("Remove Left", true, seqs, + column, viewport.getAlignment()); + viewport.setStartRes(0); + } + else + { + trimRegion = new TrimRegionCommand("Remove Right", false, seqs, + column, viewport.getAlignment()); + } + + statusBar.setText(MessageManager.formatMessage( + "label.removed_columns", + new String[] { Integer.valueOf(trimRegion.getSize()) + .toString() })); + + addHistoryItem(trimRegion); + + for (SequenceGroup sg : viewport.getAlignment().getGroups()) + { + if ((trimLeft && !sg.adjustForRemoveLeft(column)) + || (!trimLeft && !sg.adjustForRemoveRight(column))) + { + viewport.getAlignment().deleteGroup(sg); + } + } + + viewport.firePropertyChange("alignment", null, viewport + .getAlignment().getSequences()); + } + } + + /** + * DOCUMENT ME! + * + * @param e + * DOCUMENT ME! + */ + @Override + public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e) + { + int start = 0, end = viewport.getAlignment().getWidth() - 1; + + SequenceI[] seqs; + if (viewport.getSelectionGroup() != null) + { + seqs = viewport.getSelectionGroup().getSequencesAsArray( + viewport.getHiddenRepSequences()); + start = viewport.getSelectionGroup().getStartRes(); + end = viewport.getSelectionGroup().getEndRes(); + } + else + { + seqs = viewport.getAlignment().getSequencesArray(); + } + + RemoveGapColCommand removeGapCols = new RemoveGapColCommand( + "Remove Gapped Columns", seqs, start, end, + viewport.getAlignment()); + + addHistoryItem(removeGapCols); + + statusBar.setText(MessageManager.formatMessage( + "label.removed_empty_columns", + new Object[] { Integer.valueOf(removeGapCols.getSize()) + .toString() })); + + // This is to maintain viewport position on first residue + // of first sequence + SequenceI seq = viewport.getAlignment().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()); + + } + + /** + * DOCUMENT ME! + * + * @param e + * DOCUMENT ME! + */ + @Override + public void removeAllGapsMenuItem_actionPerformed(ActionEvent e) + { + int start = 0, end = viewport.getAlignment().getWidth() - 1; + + SequenceI[] seqs; + if (viewport.getSelectionGroup() != null) + { + seqs = viewport.getSelectionGroup().getSequencesAsArray( + viewport.getHiddenRepSequences()); + start = viewport.getSelectionGroup().getStartRes(); + end = viewport.getSelectionGroup().getEndRes(); + } + else + { + seqs = viewport.getAlignment().getSequencesArray(); + } + + // This is to maintain viewport position on first residue + // of first sequence + SequenceI seq = viewport.getAlignment().getSequenceAt(0); + int startRes = seq.findPosition(viewport.startRes); + + addHistoryItem(new RemoveGapsCommand("Remove Gaps", seqs, start, end, + viewport.getAlignment())); + + viewport.setStartRes(seq.findIndex(startRes) - 1); + + viewport.firePropertyChange("alignment", null, viewport.getAlignment() + .getSequences()); + + } + + /** + * DOCUMENT ME! + * + * @param e + * DOCUMENT ME! + */ + @Override + public void padGapsMenuitem_actionPerformed(ActionEvent e) + { + viewport.setPadGaps(padGapsMenuitem.isSelected()); + viewport.firePropertyChange("alignment", null, viewport.getAlignment() + .getSequences()); + } + + /** + * DOCUMENT ME! + * + * @param e + * DOCUMENT ME! + */ + @Override + public void findMenuItem_actionPerformed(ActionEvent e) + { + new Finder(); + } + + /** + * Create a new view of the current alignment. + */ + @Override + public void newView_actionPerformed(ActionEvent e) + { + newView(null, true); + } + + /** + * Creates and shows a new view of the current alignment. + * + * @param viewTitle + * title of newly created view; if null, one will be generated + * @param copyAnnotation + * if true then duplicate all annnotation, groups and settings + * @return new alignment panel, already displayed. + */ + public AlignmentPanel newView(String viewTitle, boolean copyAnnotation) + { + /* + * Create a new AlignmentPanel (with its own, new Viewport) + */ + AlignmentPanel newap = new Jalview2XML().copyAlignPanel(alignPanel, + true); + if (!copyAnnotation) + { + /* + * remove all groups and annotation except for the automatic stuff + */ + newap.av.getAlignment().deleteAllGroups(); + newap.av.getAlignment().deleteAllAnnotations(false); + } + + newap.av.setGatherViewsHere(false); + + if (viewport.viewName == null) + { + viewport.viewName = MessageManager + .getString("label.view_name_original"); + } + + /* + * Views share the same edits undo and redo stacks + */ + newap.av.setHistoryList(viewport.getHistoryList()); + newap.av.setRedoList(viewport.getRedoList()); + + /* + * Views share the same mappings; need to deregister any new mappings + * created by copyAlignPanel, and register the new reference to the shared + * mappings + */ + newap.av.replaceMappings(viewport.getAlignment()); + + newap.av.viewName = getNewViewName(viewTitle); + + addAlignmentPanel(newap, true); + newap.alignmentChanged(); + + if (alignPanels.size() == 2) + { + viewport.setGatherViewsHere(true); + } + tabbedPane.setSelectedIndex(tabbedPane.getTabCount() - 1); + return newap; + } + + /** + * Make a new name for the view, ensuring it is unique within the current + * sequenceSetId. (This used to be essential for Jalview Project archives, but + * these now use viewId. Unique view names are still desirable for usability.) + * + * @param viewTitle + * @return + */ + protected String getNewViewName(String viewTitle) + { + int index = Desktop.getViewCount(viewport.getSequenceSetId()); + boolean addFirstIndex = false; + if (viewTitle == null || viewTitle.trim().length() == 0) + { + viewTitle = MessageManager.getString("action.view"); + addFirstIndex = true; + } + else + { + index = 1;// we count from 1 if given a specific name + } + String newViewName = viewTitle + ((addFirstIndex) ? " " + index : ""); + + List comps = PaintRefresher.components.get(viewport + .getSequenceSetId()); + + List existingNames = getExistingViewNames(comps); + + while (existingNames.contains(newViewName)) + { + newViewName = viewTitle + " " + (++index); + } + return newViewName; + } + + /** + * Returns a list of distinct view names found in the given list of + * components. View names are held on the viewport of an AlignmentPanel. + * + * @param comps + * @return + */ + protected List getExistingViewNames(List comps) + { + List existingNames = new ArrayList(); + for (Component comp : comps) + { + if (comp instanceof AlignmentPanel) + { + AlignmentPanel ap = (AlignmentPanel) comp; + if (!existingNames.contains(ap.av.viewName)) + { + existingNames.add(ap.av.viewName); + } + } + } + return existingNames; + } + + /** + * Explode tabbed views into separate windows. + */ + @Override + public void expandViews_actionPerformed(ActionEvent e) + { + Desktop.instance.explodeViews(this); + } + + /** + * Gather views in separate windows back into a tabbed presentation. + */ + @Override + public void gatherViews_actionPerformed(ActionEvent e) + { + Desktop.instance.gatherViews(this); + } + + /** + * DOCUMENT ME! + * + * @param e + * DOCUMENT ME! + */ + @Override + public void font_actionPerformed(ActionEvent e) + { + new FontChooser(alignPanel); + } + + /** + * DOCUMENT ME! + * + * @param e + * DOCUMENT ME! + */ + @Override + protected void seqLimit_actionPerformed(ActionEvent e) + { + viewport.setShowJVSuffix(seqLimits.isSelected()); + + alignPanel.getIdPanel().getIdCanvas() + .setPreferredSize(alignPanel.calculateIdWidth()); + alignPanel.paintAlignment(true); + } + + @Override + public void idRightAlign_actionPerformed(ActionEvent e) + { + viewport.setRightAlignIds(idRightAlign.isSelected()); + alignPanel.paintAlignment(true); + } + + @Override + public void centreColumnLabels_actionPerformed(ActionEvent e) + { + viewport.setCentreColumnLabels(centreColumnLabelsMenuItem.getState()); + alignPanel.paintAlignment(true); + } + + /* + * (non-Javadoc) + * + * @see jalview.jbgui.GAlignFrame#followHighlight_actionPerformed() + */ + @Override + protected void followHighlight_actionPerformed() + { + /* + * Set the 'follow' flag on the Viewport (and scroll to position if now + * true). + */ + final boolean state = this.followHighlightMenuItem.getState(); + viewport.setFollowHighlight(state); + if (state) + { + alignPanel.scrollToPosition( + alignPanel.getSeqPanel().seqCanvas.searchResults, false); + } + } + + /** + * DOCUMENT ME! + * + * @param e + * DOCUMENT ME! + */ + @Override + protected void colourTextMenuItem_actionPerformed(ActionEvent e) + { + viewport.setColourText(colourTextMenuItem.isSelected()); + alignPanel.paintAlignment(true); + } + + /** + * DOCUMENT ME! + * + * @param e + * DOCUMENT ME! + */ + @Override + public void wrapMenuItem_actionPerformed(ActionEvent e) + { + scaleAbove.setVisible(wrapMenuItem.isSelected()); + scaleLeft.setVisible(wrapMenuItem.isSelected()); + scaleRight.setVisible(wrapMenuItem.isSelected()); + viewport.setWrapAlignment(wrapMenuItem.isSelected()); + alignPanel.updateLayout(); + } + + @Override + public void showAllSeqs_actionPerformed(ActionEvent e) + { + viewport.showAllHiddenSeqs(); + } + + @Override + public void showAllColumns_actionPerformed(ActionEvent e) + { + viewport.showAllHiddenColumns(); + repaint(); + viewport.sendSelection(); + } + + @Override + public void hideSelSequences_actionPerformed(ActionEvent e) + { + viewport.hideAllSelectedSeqs(); + // alignPanel.paintAlignment(true); + } + + /** + * called by key handler and the hide all/show all menu items + * + * @param toggleSeqs + * @param toggleCols + */ + private void toggleHiddenRegions(boolean toggleSeqs, boolean toggleCols) + { + + boolean hide = false; + SequenceGroup sg = viewport.getSelectionGroup(); + if (!toggleSeqs && !toggleCols) + { + // Hide everything by the current selection - this is a hack - we do the + // invert and then hide + // first check that there will be visible columns after the invert. + if ((viewport.getColumnSelection() != null + && viewport.getColumnSelection().getSelected() != null && viewport + .getColumnSelection().getSelected().size() > 0) + || (sg != null && sg.getSize() > 0 && sg.getStartRes() <= sg + .getEndRes())) + { + // now invert the sequence set, if required - empty selection implies + // that no hiding is required. + if (sg != null) + { + invertSequenceMenuItem_actionPerformed(null); + sg = viewport.getSelectionGroup(); + toggleSeqs = true; + + } + viewport.expandColSelection(sg, true); + // finally invert the column selection and get the new sequence + // selection. + invertColSel_actionPerformed(null); + toggleCols = true; + } + } + + if (toggleSeqs) + { + if (sg != null && sg.getSize() != viewport.getAlignment().getHeight()) + { + hideSelSequences_actionPerformed(null); + hide = true; + } + else if (!(toggleCols && viewport.getColumnSelection().getSelected() + .size() > 0)) + { + showAllSeqs_actionPerformed(null); + } + } + + if (toggleCols) + { + if (viewport.getColumnSelection().getSelected().size() > 0) + { + hideSelColumns_actionPerformed(null); + if (!toggleSeqs) + { + viewport.setSelectionGroup(sg); + } + } + else if (!hide) + { + showAllColumns_actionPerformed(null); + } + } + } + + /* + * (non-Javadoc) + * + * @see + * jalview.jbgui.GAlignFrame#hideAllButSelection_actionPerformed(java.awt. + * event.ActionEvent) + */ + @Override + public void hideAllButSelection_actionPerformed(ActionEvent e) + { + toggleHiddenRegions(false, false); + viewport.sendSelection(); + } + + /* + * (non-Javadoc) + * + * @see + * jalview.jbgui.GAlignFrame#hideAllSelection_actionPerformed(java.awt.event + * .ActionEvent) + */ + @Override + public void hideAllSelection_actionPerformed(ActionEvent e) + { + SequenceGroup sg = viewport.getSelectionGroup(); + viewport.expandColSelection(sg, false); + viewport.hideAllSelectedSeqs(); + viewport.hideSelectedColumns(); + alignPanel.paintAlignment(true); + viewport.sendSelection(); + } + + /* + * (non-Javadoc) + * + * @see + * jalview.jbgui.GAlignFrame#showAllhidden_actionPerformed(java.awt.event. + * ActionEvent) + */ + @Override + public void showAllhidden_actionPerformed(ActionEvent e) + { + viewport.showAllHiddenColumns(); + viewport.showAllHiddenSeqs(); + alignPanel.paintAlignment(true); + viewport.sendSelection(); + } + + @Override + public void hideSelColumns_actionPerformed(ActionEvent e) + { + viewport.hideSelectedColumns(); + alignPanel.paintAlignment(true); + viewport.sendSelection(); + } + + @Override + public void hiddenMarkers_actionPerformed(ActionEvent e) + { + viewport.setShowHiddenMarkers(hiddenMarkers.isSelected()); + repaint(); + } + + /** + * DOCUMENT ME! + * + * @param e + * DOCUMENT ME! + */ + @Override + protected void scaleAbove_actionPerformed(ActionEvent e) + { + viewport.setScaleAboveWrapped(scaleAbove.isSelected()); + alignPanel.paintAlignment(true); + } + + /** + * DOCUMENT ME! + * + * @param e + * DOCUMENT ME! + */ + @Override + protected void scaleLeft_actionPerformed(ActionEvent e) + { + viewport.setScaleLeftWrapped(scaleLeft.isSelected()); + alignPanel.paintAlignment(true); + } + + /** + * DOCUMENT ME! + * + * @param e + * DOCUMENT ME! + */ + @Override + protected void scaleRight_actionPerformed(ActionEvent e) + { + viewport.setScaleRightWrapped(scaleRight.isSelected()); + alignPanel.paintAlignment(true); + } + + /** + * DOCUMENT ME! + * + * @param e + * DOCUMENT ME! + */ + @Override + public void viewBoxesMenuItem_actionPerformed(ActionEvent e) + { + viewport.setShowBoxes(viewBoxesMenuItem.isSelected()); + alignPanel.paintAlignment(true); + } + + /** + * DOCUMENT ME! + * + * @param e + * DOCUMENT ME! + */ + @Override + public void viewTextMenuItem_actionPerformed(ActionEvent e) + { + viewport.setShowText(viewTextMenuItem.isSelected()); + alignPanel.paintAlignment(true); + } + + /** + * DOCUMENT ME! + * + * @param e + * DOCUMENT ME! + */ + @Override + protected void renderGapsMenuItem_actionPerformed(ActionEvent e) + { + viewport.setRenderGaps(renderGapsMenuItem.isSelected()); + alignPanel.paintAlignment(true); + } + + public FeatureSettings featureSettings; + + @Override + public FeatureSettingsControllerI getFeatureSettingsUI() + { + return featureSettings; + } + + @Override + public void featureSettings_actionPerformed(ActionEvent e) + { + if (featureSettings != null) + { + featureSettings.close(); + featureSettings = null; + } + if (!showSeqFeatures.isSelected()) + { + // make sure features are actually displayed + showSeqFeatures.setSelected(true); + showSeqFeatures_actionPerformed(null); + } + featureSettings = new FeatureSettings(this); + } + + /** + * Set or clear 'Show Sequence Features' + * + * @param evt + * DOCUMENT ME! + */ + @Override + public void showSeqFeatures_actionPerformed(ActionEvent evt) + { + viewport.setShowSequenceFeatures(showSeqFeatures.isSelected()); + alignPanel.paintAlignment(true); + if (alignPanel.getOverviewPanel() != null) + { + alignPanel.getOverviewPanel().updateOverviewImage(); + } + } + + /** + * Set or clear 'Show Sequence Features' + * + * @param evt + * DOCUMENT ME! + */ + @Override + public void showSeqFeaturesHeight_actionPerformed(ActionEvent evt) + { + viewport.setShowSequenceFeaturesHeight(showSeqFeaturesHeight + .isSelected()); + if (viewport.isShowSequenceFeaturesHeight()) + { + // ensure we're actually displaying features + viewport.setShowSequenceFeatures(true); + showSeqFeatures.setSelected(true); + } + alignPanel.paintAlignment(true); + if (alignPanel.getOverviewPanel() != null) + { + alignPanel.getOverviewPanel().updateOverviewImage(); + } + } + + /** + * Action on toggle of the 'Show annotations' menu item. This shows or hides + * the annotations panel as a whole. + * + * The options to show/hide all annotations should be enabled when the panel + * is shown, and disabled when the panel is hidden. + * + * @param e + */ + @Override + public void annotationPanelMenuItem_actionPerformed(ActionEvent e) + { + final boolean setVisible = annotationPanelMenuItem.isSelected(); + viewport.setShowAnnotation(setVisible); + this.showAllSeqAnnotations.setEnabled(setVisible); + this.hideAllSeqAnnotations.setEnabled(setVisible); + this.showAllAlAnnotations.setEnabled(setVisible); + this.hideAllAlAnnotations.setEnabled(setVisible); + alignPanel.updateLayout(); + } + + @Override + public void alignmentProperties() + { + JEditorPane editPane = new JEditorPane("text/html", ""); + editPane.setEditable(false); + StringBuffer contents = new AlignmentProperties(viewport.getAlignment()) + .formatAsHtml(); + editPane.setText(MessageManager.formatMessage("label.html_content", + new Object[] { contents.toString() })); + JInternalFrame frame = new JInternalFrame(); + frame.getContentPane().add(new JScrollPane(editPane)); + + Desktop.addInternalFrame(frame, MessageManager.formatMessage( + "label.alignment_properties", new Object[] { getTitle() }), + 500, 400); + } + + /** + * DOCUMENT ME! + * + * @param e + * DOCUMENT ME! + */ + @Override + public void overviewMenuItem_actionPerformed(ActionEvent e) + { + if (alignPanel.overviewPanel != null) + { + return; + } + + JInternalFrame frame = new JInternalFrame(); + OverviewPanel overview = new OverviewPanel(alignPanel); + frame.setContentPane(overview); + Desktop.addInternalFrame(frame, MessageManager.formatMessage( + "label.overview_params", new Object[] { this.getTitle() }), + frame.getWidth(), frame.getHeight()); + frame.pack(); + frame.setLayer(JLayeredPane.PALETTE_LAYER); + frame.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter() + { + @Override + public void internalFrameClosed( + javax.swing.event.InternalFrameEvent evt) + { + alignPanel.setOverviewPanel(null); + }; + }); + + alignPanel.setOverviewPanel(overview); + } + + @Override + public void textColour_actionPerformed(ActionEvent e) + { + new TextColourChooser().chooseColour(alignPanel, null); + } + + /** + * DOCUMENT ME! + * + * @param e + * DOCUMENT ME! + */ + @Override + protected void noColourmenuItem_actionPerformed(ActionEvent e) + { + changeColour(null); + } + + /** + * DOCUMENT ME! + * + * @param e + * DOCUMENT ME! + */ + @Override + public void clustalColour_actionPerformed(ActionEvent e) + { + changeColour(new ClustalxColourScheme(viewport.getAlignment(), + viewport.getHiddenRepSequences())); + } + + /** + * DOCUMENT ME! + * + * @param e + * DOCUMENT ME! + */ + @Override + public void zappoColour_actionPerformed(ActionEvent e) + { + changeColour(new ZappoColourScheme()); + } + + /** + * DOCUMENT ME! + * + * @param e + * DOCUMENT ME! + */ + @Override + public void taylorColour_actionPerformed(ActionEvent e) + { + changeColour(new TaylorColourScheme()); + } + + /** + * DOCUMENT ME! + * + * @param e + * DOCUMENT ME! + */ + @Override + public void hydrophobicityColour_actionPerformed(ActionEvent e) + { + changeColour(new HydrophobicColourScheme()); + } + + /** + * DOCUMENT ME! + * + * @param e + * DOCUMENT ME! + */ + @Override + public void helixColour_actionPerformed(ActionEvent e) + { + changeColour(new HelixColourScheme()); + } + + /** + * DOCUMENT ME! + * + * @param e + * DOCUMENT ME! + */ + @Override + public void strandColour_actionPerformed(ActionEvent e) + { + changeColour(new StrandColourScheme()); + } + + /** + * DOCUMENT ME! + * + * @param e + * DOCUMENT ME! + */ + @Override + public void turnColour_actionPerformed(ActionEvent e) + { + changeColour(new TurnColourScheme()); + } + + /** + * DOCUMENT ME! + * + * @param e + * DOCUMENT ME! + */ + @Override + public void buriedColour_actionPerformed(ActionEvent e) + { + changeColour(new BuriedColourScheme()); + } + + /** + * DOCUMENT ME! + * + * @param e + * DOCUMENT ME! + */ + @Override + public void nucleotideColour_actionPerformed(ActionEvent e) + { + changeColour(new NucleotideColourScheme()); + } + + @Override + public void purinePyrimidineColour_actionPerformed(ActionEvent e) + { + changeColour(new PurinePyrimidineColourScheme()); + } + + /* + * public void covariationColour_actionPerformed(ActionEvent e) { + * changeColour(new + * CovariationColourScheme(viewport.getAlignment().getAlignmentAnnotation + * ()[0])); } + */ + @Override + public void annotationColour_actionPerformed(ActionEvent e) + { + new AnnotationColourChooser(viewport, alignPanel); + } + + @Override + public void annotationColumn_actionPerformed(ActionEvent e) + { + new AnnotationColumnChooser(viewport, alignPanel); + } + + @Override + public void rnahelicesColour_actionPerformed(ActionEvent e) + { + new RNAHelicesColourChooser(viewport, alignPanel); + } + + /** + * DOCUMENT ME! + * + * @param e + * DOCUMENT ME! + */ + @Override + protected void applyToAllGroups_actionPerformed(ActionEvent e) + { + viewport.setColourAppliesToAllGroups(applyToAllGroups.isSelected()); + } + + /** + * DOCUMENT ME! + * + * @param cs + * DOCUMENT ME! + */ + @Override + public void changeColour(ColourSchemeI cs) + { + // TODO: pull up to controller method + + if (cs != null) + { + // Make sure viewport is up to date w.r.t. any sliders + if (viewport.getAbovePIDThreshold()) + { + int threshold = SliderPanel.setPIDSliderSource(alignPanel, cs, + "Background"); + viewport.setThreshold(threshold); + } + + if (viewport.getConservationSelected()) + { + cs.setConservationInc(SliderPanel.setConservationSlider(alignPanel, + cs, "Background")); + } + if (cs instanceof TCoffeeColourScheme) + { + tcoffeeColour.setEnabled(true); + tcoffeeColour.setSelected(true); + } + } + + viewport.setGlobalColourScheme(cs); + + alignPanel.paintAlignment(true); + } + + /** + * DOCUMENT ME! + * + * @param e + * DOCUMENT ME! + */ + @Override + protected void modifyPID_actionPerformed(ActionEvent e) + { + if (viewport.getAbovePIDThreshold() + && viewport.getGlobalColourScheme() != null) + { + SliderPanel.setPIDSliderSource(alignPanel, + viewport.getGlobalColourScheme(), "Background"); + SliderPanel.showPIDSlider(); + } + } + + /** + * DOCUMENT ME! + * + * @param e + * DOCUMENT ME! + */ + @Override + protected void modifyConservation_actionPerformed(ActionEvent e) + { + if (viewport.getConservationSelected() + && viewport.getGlobalColourScheme() != null) + { + SliderPanel.setConservationSlider(alignPanel, + viewport.getGlobalColourScheme(), "Background"); + SliderPanel.showConservationSlider(); + } + } + + /** + * DOCUMENT ME! + * + * @param e + * DOCUMENT ME! + */ + @Override + protected void conservationMenuItem_actionPerformed(ActionEvent e) + { + viewport.setConservationSelected(conservationMenuItem.isSelected()); + + viewport.setAbovePIDThreshold(false); + abovePIDThreshold.setSelected(false); + + changeColour(viewport.getGlobalColourScheme()); + + modifyConservation_actionPerformed(null); + } + + /** + * DOCUMENT ME! + * + * @param e + * DOCUMENT ME! + */ + @Override + public void abovePIDThreshold_actionPerformed(ActionEvent e) + { + viewport.setAbovePIDThreshold(abovePIDThreshold.isSelected()); + + conservationMenuItem.setSelected(false); + viewport.setConservationSelected(false); + + changeColour(viewport.getGlobalColourScheme()); + + modifyPID_actionPerformed(null); + } + + /** + * DOCUMENT ME! + * + * @param e + * DOCUMENT ME! + */ + @Override + public void userDefinedColour_actionPerformed(ActionEvent e) + { + if (e.getActionCommand().equals( + MessageManager.getString("action.user_defined"))) + { + new UserDefinedColours(alignPanel, null); + } + else + { + UserColourScheme udc = (UserColourScheme) UserDefinedColours + .getUserColourSchemes().get(e.getActionCommand()); + + changeColour(udc); + } + } + + public void updateUserColourMenu() + { + + Component[] menuItems = colourMenu.getMenuComponents(); + int iSize = menuItems.length; + for (int i = 0; i < iSize; i++) + { + if (menuItems[i].getName() != null + && menuItems[i].getName().equals("USER_DEFINED")) + { + colourMenu.remove(menuItems[i]); + iSize--; + } + } + if (jalview.gui.UserDefinedColours.getUserColourSchemes() != null) + { + java.util.Enumeration userColours = jalview.gui.UserDefinedColours + .getUserColourSchemes().keys(); + + while (userColours.hasMoreElements()) + { + final JRadioButtonMenuItem radioItem = new JRadioButtonMenuItem( + userColours.nextElement().toString()); + radioItem.setName("USER_DEFINED"); + radioItem.addMouseListener(new MouseAdapter() + { + @Override + public void mousePressed(MouseEvent evt) + { + if (evt.isPopupTrigger()) + { + radioItem.removeActionListener(radioItem.getActionListeners()[0]); + + int option = JOptionPane.showInternalConfirmDialog( + jalview.gui.Desktop.desktop, + MessageManager + .getString("label.remove_from_default_list"), + MessageManager + .getString("label.remove_user_defined_colour"), + JOptionPane.YES_NO_OPTION); + if (option == JOptionPane.YES_OPTION) + { + jalview.gui.UserDefinedColours + .removeColourFromDefaults(radioItem.getText()); + colourMenu.remove(radioItem); + } + else + { + radioItem.addActionListener(new ActionListener() + { + @Override + public void actionPerformed(ActionEvent evt) + { + userDefinedColour_actionPerformed(evt); + } + }); + } + } + } + }); + radioItem.addActionListener(new ActionListener() + { + @Override + public void actionPerformed(ActionEvent evt) + { + userDefinedColour_actionPerformed(evt); + } + }); + + colourMenu.insert(radioItem, 15); + colours.add(radioItem); + } + } + } + + /** + * DOCUMENT ME! + * + * @param e + * DOCUMENT ME! + */ + @Override + public void PIDColour_actionPerformed(ActionEvent e) + { + changeColour(new PIDColourScheme()); + } + + /** + * DOCUMENT ME! + * + * @param e + * DOCUMENT ME! + */ + @Override + public void BLOSUM62Colour_actionPerformed(ActionEvent e) + { + changeColour(new Blosum62ColourScheme()); + } + + /** + * DOCUMENT ME! + * + * @param e + * DOCUMENT ME! + */ + @Override + public void sortPairwiseMenuItem_actionPerformed(ActionEvent e) + { + SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray(); + AlignmentSorter.sortByPID(viewport.getAlignment(), viewport + .getAlignment().getSequenceAt(0), null); + addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder, + viewport.getAlignment())); + alignPanel.paintAlignment(true); + } + + /** + * DOCUMENT ME! + * + * @param e + * DOCUMENT ME! + */ + @Override + public void sortIDMenuItem_actionPerformed(ActionEvent e) + { + SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray(); + AlignmentSorter.sortByID(viewport.getAlignment()); + addHistoryItem(new OrderCommand("ID Sort", oldOrder, + viewport.getAlignment())); + alignPanel.paintAlignment(true); + } + + /** + * DOCUMENT ME! + * + * @param e + * DOCUMENT ME! + */ + @Override + public void sortLengthMenuItem_actionPerformed(ActionEvent e) + { + SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray(); + AlignmentSorter.sortByLength(viewport.getAlignment()); + addHistoryItem(new OrderCommand("Length Sort", oldOrder, + viewport.getAlignment())); + alignPanel.paintAlignment(true); + } + + /** + * DOCUMENT ME! + * + * @param e + * DOCUMENT ME! + */ + @Override + public void sortGroupMenuItem_actionPerformed(ActionEvent e) + { + SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray(); + AlignmentSorter.sortByGroup(viewport.getAlignment()); + addHistoryItem(new OrderCommand("Group Sort", oldOrder, + viewport.getAlignment())); + + alignPanel.paintAlignment(true); + } + + /** + * DOCUMENT ME! + * + * @param e + * DOCUMENT ME! + */ + @Override + public void removeRedundancyMenuItem_actionPerformed(ActionEvent e) + { + new RedundancyPanel(alignPanel, this); + } + + /** + * DOCUMENT ME! + * + * @param e + * DOCUMENT ME! + */ + @Override + public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e) + { + if ((viewport.getSelectionGroup() == null) + || (viewport.getSelectionGroup().getSize() < 2)) + { + JOptionPane.showInternalMessageDialog(this, MessageManager + .getString("label.you_must_select_least_two_sequences"), + MessageManager.getString("label.invalid_selection"), + JOptionPane.WARNING_MESSAGE); + } + else + { + JInternalFrame frame = new JInternalFrame(); + frame.setContentPane(new PairwiseAlignPanel(viewport)); + Desktop.addInternalFrame(frame, + MessageManager.getString("action.pairwise_alignment"), 600, + 500); + } + } + + /** + * DOCUMENT ME! + * + * @param e + * DOCUMENT ME! + */ + @Override + public void PCAMenuItem_actionPerformed(ActionEvent e) + { + if (((viewport.getSelectionGroup() != null) + && (viewport.getSelectionGroup().getSize() < 4) && (viewport + .getSelectionGroup().getSize() > 0)) + || (viewport.getAlignment().getHeight() < 4)) + { + JOptionPane + .showInternalMessageDialog( + this, + MessageManager + .getString("label.principal_component_analysis_must_take_least_four_input_sequences"), + MessageManager + .getString("label.sequence_selection_insufficient"), + JOptionPane.WARNING_MESSAGE); + + return; + } + + new PCAPanel(alignPanel); + } + + @Override + public void autoCalculate_actionPerformed(ActionEvent e) + { + viewport.autoCalculateConsensus = autoCalculate.isSelected(); + if (viewport.autoCalculateConsensus) + { + viewport.firePropertyChange("alignment", null, viewport + .getAlignment().getSequences()); + } + } + + @Override + public void sortByTreeOption_actionPerformed(ActionEvent e) + { + viewport.sortByTree = sortByTree.isSelected(); + } + + @Override + protected void listenToViewSelections_actionPerformed(ActionEvent e) + { + viewport.followSelection = listenToViewSelections.isSelected(); + } + + /** + * DOCUMENT ME! + * + * @param e + * DOCUMENT ME! + */ + @Override + public void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e) + { + newTreePanel("AV", "PID", "Average distance tree using PID"); + } + + /** + * DOCUMENT ME! + * + * @param e + * DOCUMENT ME! + */ + @Override + public void neighbourTreeMenuItem_actionPerformed(ActionEvent e) + { + newTreePanel("NJ", "PID", "Neighbour joining tree using PID"); + } + + /** + * DOCUMENT ME! + * + * @param e + * DOCUMENT ME! + */ + @Override + protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e) + { + newTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62"); + } + + /** + * DOCUMENT ME! + * + * @param e + * DOCUMENT ME! + */ + @Override + protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e) + { + newTreePanel("AV", "BL", "Average distance tree using BLOSUM62"); + } + + /** + * DOCUMENT ME! + * + * @param type + * DOCUMENT ME! + * @param pwType + * DOCUMENT ME! + * @param title + * DOCUMENT ME! + */ + void newTreePanel(String type, String pwType, String title) + { + TreePanel tp; + + if (viewport.getSelectionGroup() != null + && viewport.getSelectionGroup().getSize() > 0) + { + if (viewport.getSelectionGroup().getSize() < 3) + { + JOptionPane + .showMessageDialog( + Desktop.desktop, + MessageManager + .getString("label.you_need_more_two_sequences_selected_build_tree"), + MessageManager + .getString("label.not_enough_sequences"), + JOptionPane.WARNING_MESSAGE); + return; + } + + SequenceGroup sg = viewport.getSelectionGroup(); + + /* Decide if the selection is a column region */ + for (SequenceI _s : sg.getSequences()) + { + if (_s.getLength() < sg.getEndRes()) + { + JOptionPane + .showMessageDialog( + Desktop.desktop, + MessageManager + .getString("label.selected_region_to_tree_may_only_contain_residues_or_gaps"), + MessageManager + .getString("label.sequences_selection_not_aligned"), + JOptionPane.WARNING_MESSAGE); + + return; + } + } + + title = title + " on region"; + tp = new TreePanel(alignPanel, type, pwType); + } + else + { + // are the visible sequences aligned? + if (!viewport.getAlignment().isAligned(false)) + { + JOptionPane + .showMessageDialog( + Desktop.desktop, + MessageManager + .getString("label.sequences_must_be_aligned_before_creating_tree"), + MessageManager + .getString("label.sequences_not_aligned"), + JOptionPane.WARNING_MESSAGE); + + return; + } + + if (viewport.getAlignment().getHeight() < 2) + { + return; + } + + tp = new TreePanel(alignPanel, type, pwType); + } + + title += " from "; + + if (viewport.viewName != null) + { + title += viewport.viewName + " of "; + } + + title += this.title; + + Desktop.addInternalFrame(tp, title, 600, 500); + } + + /** + * DOCUMENT ME! + * + * @param title + * DOCUMENT ME! + * @param order + * DOCUMENT ME! + */ + public void addSortByOrderMenuItem(String title, + final AlignmentOrder order) + { + final JMenuItem item = new JMenuItem(MessageManager.formatMessage( + "action.by_title_param", new Object[] { title })); + sort.add(item); + item.addActionListener(new java.awt.event.ActionListener() + { + @Override + public void actionPerformed(ActionEvent e) + { + SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray(); + + // TODO: JBPNote - have to map order entries to curent SequenceI + // pointers + AlignmentSorter.sortBy(viewport.getAlignment(), order); + + addHistoryItem(new OrderCommand(order.getName(), oldOrder, viewport + .getAlignment())); + + alignPanel.paintAlignment(true); + } + }); + } + + /** + * Add a new sort by annotation score menu item + * + * @param sort + * the menu to add the option to + * @param scoreLabel + * the label used to retrieve scores for each sequence on the + * alignment + */ + public void addSortByAnnotScoreMenuItem(JMenu sort, + final String scoreLabel) + { + final JMenuItem item = new JMenuItem(scoreLabel); + sort.add(item); + item.addActionListener(new java.awt.event.ActionListener() + { + @Override + public void actionPerformed(ActionEvent e) + { + SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray(); + AlignmentSorter.sortByAnnotationScore(scoreLabel, + viewport.getAlignment());// ,viewport.getSelectionGroup()); + addHistoryItem(new OrderCommand("Sort by " + scoreLabel, oldOrder, + viewport.getAlignment())); + alignPanel.paintAlignment(true); + } + }); + } + + /** + * last hash for alignment's annotation array - used to minimise cost of + * rebuild. + */ + protected int _annotationScoreVectorHash; + + /** + * search the alignment and rebuild the sort by annotation score submenu the + * last alignment annotation vector hash is stored to minimize cost of + * rebuilding in subsequence calls. + * + */ + @Override + public void buildSortByAnnotationScoresMenu() + { + if (viewport.getAlignment().getAlignmentAnnotation() == null) + { + return; + } + + if (viewport.getAlignment().getAlignmentAnnotation().hashCode() != _annotationScoreVectorHash) + { + sortByAnnotScore.removeAll(); + // almost certainly a quicker way to do this - but we keep it simple + Hashtable scoreSorts = new Hashtable(); + AlignmentAnnotation aann[]; + for (SequenceI sqa : viewport.getAlignment().getSequences()) + { + aann = sqa.getAnnotation(); + for (int i = 0; aann != null && i < aann.length; i++) + { + if (aann[i].hasScore() && aann[i].sequenceRef != null) + { + scoreSorts.put(aann[i].label, aann[i].label); + } + } + } + Enumeration labels = scoreSorts.keys(); + while (labels.hasMoreElements()) + { + addSortByAnnotScoreMenuItem(sortByAnnotScore, + (String) labels.nextElement()); + } + sortByAnnotScore.setVisible(scoreSorts.size() > 0); + scoreSorts.clear(); + + _annotationScoreVectorHash = viewport.getAlignment() + .getAlignmentAnnotation().hashCode(); + } + } + + /** + * Maintain the Order by->Displayed Tree menu. Creates a new menu item for a + * TreePanel with an appropriate jalview.analysis.AlignmentSorter + * call. Listeners are added to remove the menu item when the treePanel is + * closed, and adjust the tree leaf to sequence mapping when the alignment is + * modified. + * + * @param treePanel + * Displayed tree window. + * @param title + * SortBy menu item title. + */ + @Override + public void buildTreeMenu() + { + calculateTree.removeAll(); + // build the calculate menu + + for (final String type : new String[] { "NJ", "AV" }) + { + String treecalcnm = MessageManager.getString("label.tree_calc_" + + type.toLowerCase()); + for (final String pwtype : ResidueProperties.scoreMatrices.keySet()) + { + JMenuItem tm = new JMenuItem(); + ScoreModelI sm = ResidueProperties.scoreMatrices.get(pwtype); + if (sm.isDNA() == viewport.getAlignment().isNucleotide() + || sm.isProtein() == !viewport.getAlignment() + .isNucleotide()) + { + String smn = MessageManager.getStringOrReturn( + "label.score_model_", sm.getName()); + final String title = MessageManager.formatMessage( + "label.treecalc_title", treecalcnm, smn); + tm.setText(title);// + tm.addActionListener(new java.awt.event.ActionListener() + { + @Override + public void actionPerformed(ActionEvent e) + { + newTreePanel(type, pwtype, title); + } + }); + calculateTree.add(tm); + } + + } + } + sortByTreeMenu.removeAll(); + + List comps = PaintRefresher.components.get(viewport + .getSequenceSetId()); + List treePanels = new ArrayList(); + for (Component comp : comps) + { + if (comp instanceof TreePanel) + { + treePanels.add((TreePanel) comp); + } + } + + if (treePanels.size() < 1) + { + sortByTreeMenu.setVisible(false); + return; + } + + sortByTreeMenu.setVisible(true); + + for (final TreePanel tp : treePanels) + { + final JMenuItem item = new JMenuItem(tp.getTitle()); + item.addActionListener(new java.awt.event.ActionListener() + { + @Override + public void actionPerformed(ActionEvent e) + { + tp.sortByTree_actionPerformed(); + addHistoryItem(tp.sortAlignmentIn(alignPanel)); + + } + }); + + sortByTreeMenu.add(item); + } + } + + public boolean sortBy(AlignmentOrder alorder, String undoname) + { + SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray(); + AlignmentSorter.sortBy(viewport.getAlignment(), alorder); + if (undoname != null) + { + addHistoryItem(new OrderCommand(undoname, oldOrder, + viewport.getAlignment())); + } + alignPanel.paintAlignment(true); + return true; + } + + /** + * Work out whether the whole set of sequences or just the selected set will + * be submitted for multiple alignment. + * + */ + public jalview.datamodel.AlignmentView gatherSequencesForAlignment() + { + // Now, check we have enough sequences + AlignmentView msa = null; + + if ((viewport.getSelectionGroup() != null) + && (viewport.getSelectionGroup().getSize() > 1)) + { + // JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to + // some common interface! + /* + * SequenceGroup seqs = viewport.getSelectionGroup(); int sz; msa = new + * SequenceI[sz = seqs.getSize(false)]; + * + * for (int i = 0; i < sz; i++) { msa[i] = (SequenceI) + * seqs.getSequenceAt(i); } + */ + msa = viewport.getAlignmentView(true); + } + else if (viewport.getSelectionGroup() != null + && viewport.getSelectionGroup().getSize() == 1) + { + int option = JOptionPane.showConfirmDialog(this, + MessageManager.getString("warn.oneseq_msainput_selection"), + MessageManager.getString("label.invalid_selection"), + JOptionPane.OK_CANCEL_OPTION); + if (option == JOptionPane.OK_OPTION) + { + msa = viewport.getAlignmentView(false); + } + } + else + { + msa = viewport.getAlignmentView(false); + } + return msa; + } + + /** + * Decides what is submitted to a secondary structure prediction service: the + * first sequence in the alignment, or in the current selection, or, if the + * alignment is 'aligned' (ie padded with gaps), then the currently selected + * region or the whole alignment. (where the first sequence in the set is the + * one that the prediction will be for). + */ + public AlignmentView gatherSeqOrMsaForSecStrPrediction() + { + AlignmentView seqs = null; + + if ((viewport.getSelectionGroup() != null) + && (viewport.getSelectionGroup().getSize() > 0)) + { + seqs = viewport.getAlignmentView(true); + } + else + { + seqs = viewport.getAlignmentView(false); + } + // limit sequences - JBPNote in future - could spawn multiple prediction + // jobs + // TODO: viewport.getAlignment().isAligned is a global state - the local + // selection may well be aligned - we preserve 2.0.8 behaviour for moment. + if (!viewport.getAlignment().isAligned(false)) + { + seqs.setSequences(new SeqCigar[] { seqs.getSequences()[0] }); + // TODO: if seqs.getSequences().length>1 then should really have warned + // user! + + } + return seqs; + } + + /** + * DOCUMENT ME! + * + * @param e + * DOCUMENT ME! + */ + @Override + protected void loadTreeMenuItem_actionPerformed(ActionEvent e) + { + // Pick the tree file + JalviewFileChooser chooser = new JalviewFileChooser( + jalview.bin.Cache.getProperty("LAST_DIRECTORY")); + chooser.setFileView(new JalviewFileView()); + chooser.setDialogTitle(MessageManager + .getString("label.select_newick_like_tree_file")); + chooser.setToolTipText(MessageManager.getString("label.load_tree_file")); + + int value = chooser.showOpenDialog(null); + + if (value == JalviewFileChooser.APPROVE_OPTION) + { + String choice = chooser.getSelectedFile().getPath(); + jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice); + jalview.io.NewickFile fin = null; + try + { + fin = new jalview.io.NewickFile(choice, "File"); + viewport.setCurrentTree(ShowNewickTree(fin, choice).getTree()); + } catch (Exception ex) + { + JOptionPane + .showMessageDialog( + Desktop.desktop, + ex.getMessage(), + MessageManager + .getString("label.problem_reading_tree_file"), + JOptionPane.WARNING_MESSAGE); + ex.printStackTrace(); + } + if (fin != null && fin.hasWarningMessage()) + { + JOptionPane.showMessageDialog(Desktop.desktop, fin + .getWarningMessage(), MessageManager + .getString("label.possible_problem_with_tree_file"), + JOptionPane.WARNING_MESSAGE); + } + } + } + + @Override + protected void tcoffeeColorScheme_actionPerformed(ActionEvent e) + { + changeColour(new TCoffeeColourScheme(alignPanel.getAlignment())); + } + + public TreePanel ShowNewickTree(NewickFile nf, String title) + { + return ShowNewickTree(nf, title, 600, 500, 4, 5); + } + + public TreePanel ShowNewickTree(NewickFile nf, String title, + AlignmentView input) + { + return ShowNewickTree(nf, title, input, 600, 500, 4, 5); + } + + public TreePanel ShowNewickTree(NewickFile nf, String title, int w, + int h, int x, int y) + { + return ShowNewickTree(nf, title, null, w, h, x, y); + } + + /** + * Add a treeviewer for the tree extracted from a newick file object to the + * current alignment view + * + * @param nf + * the tree + * @param title + * tree viewer title + * @param input + * Associated alignment input data (or null) + * @param w + * width + * @param h + * height + * @param x + * position + * @param y + * position + * @return TreePanel handle + */ + public TreePanel ShowNewickTree(NewickFile nf, String title, + AlignmentView input, int w, int h, int x, int y) + { + TreePanel tp = null; + + try + { + nf.parse(); + + if (nf.getTree() != null) + { + tp = new TreePanel(alignPanel, "FromFile", title, nf, input); + + tp.setSize(w, h); + + if (x > 0 && y > 0) + { + tp.setLocation(x, y); + } + + Desktop.addInternalFrame(tp, title, w, h); + } + } catch (Exception ex) + { + ex.printStackTrace(); + } + + return tp; + } + + private boolean buildingMenu = false; + + /** + * Generates menu items and listener event actions for web service clients + * + */ + public void BuildWebServiceMenu() + { + while (buildingMenu) + { + try + { + System.err.println("Waiting for building menu to finish."); + Thread.sleep(10); + } catch (Exception e) + { + } + } + final AlignFrame me = this; + buildingMenu = true; + new Thread(new Runnable() + { + @Override + public void run() + { + final List legacyItems = new ArrayList(); + try + { + // System.err.println("Building ws menu again " + // + Thread.currentThread()); + // TODO: add support for context dependent disabling of services based + // on + // alignment and current selection + // TODO: add additional serviceHandle parameter to specify abstract + // handler + // class independently of AbstractName + // TODO: add in rediscovery GUI function to restart discoverer + // TODO: group services by location as well as function and/or + // introduce + // object broker mechanism. + final Vector wsmenu = new Vector(); + final IProgressIndicator af = me; + final JMenu msawsmenu = new JMenu("Alignment"); + final JMenu secstrmenu = new JMenu( + "Secondary Structure Prediction"); + final JMenu seqsrchmenu = new JMenu("Sequence Database Search"); + final JMenu analymenu = new JMenu("Analysis"); + final JMenu dismenu = new JMenu("Protein Disorder"); + // final JMenu msawsmenu = new + // JMenu(MessageManager.getString("label.alignment")); + // final JMenu secstrmenu = new + // JMenu(MessageManager.getString("label.secondary_structure_prediction")); + // final JMenu seqsrchmenu = new + // JMenu(MessageManager.getString("label.sequence_database_search")); + // final JMenu analymenu = new + // JMenu(MessageManager.getString("label.analysis")); + // final JMenu dismenu = new + // JMenu(MessageManager.getString("label.protein_disorder")); + // JAL-940 - only show secondary structure prediction services from + // the legacy server + if (// Cache.getDefault("SHOW_JWS1_SERVICES", true) + // && + Discoverer.services != null && (Discoverer.services.size() > 0)) + { + // TODO: refactor to allow list of AbstractName/Handler bindings to + // be + // stored or retrieved from elsewhere + // No MSAWS used any more: + // Vector msaws = null; // (Vector) + // Discoverer.services.get("MsaWS"); + Vector secstrpr = (Vector) Discoverer.services + .get("SecStrPred"); + if (secstrpr != null) + { + // Add any secondary structure prediction services + for (int i = 0, j = secstrpr.size(); i < j; i++) + { + final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle) secstrpr + .get(i); + jalview.ws.WSMenuEntryProviderI impl = jalview.ws.jws1.Discoverer + .getServiceClient(sh); + int p = secstrmenu.getItemCount(); + impl.attachWSMenuEntry(secstrmenu, me); + int q = secstrmenu.getItemCount(); + for (int litm = p; litm < q; litm++) + { + legacyItems.add(secstrmenu.getItem(litm)); + } + } + } + } + + // Add all submenus in the order they should appear on the web + // services menu + wsmenu.add(msawsmenu); + wsmenu.add(secstrmenu); + wsmenu.add(dismenu); + wsmenu.add(analymenu); + // No search services yet + // wsmenu.add(seqsrchmenu); + + javax.swing.SwingUtilities.invokeLater(new Runnable() + { + @Override + public void run() + { + try + { + webService.removeAll(); + // first, add discovered services onto the webservices menu + if (wsmenu.size() > 0) + { + for (int i = 0, j = wsmenu.size(); i < j; i++) + { + webService.add(wsmenu.get(i)); + } + } + else + { + webService.add(me.webServiceNoServices); + } + // TODO: move into separate menu builder class. + boolean new_sspred = false; + if (Cache.getDefault("SHOW_JWS2_SERVICES", true)) + { + Jws2Discoverer jws2servs = Jws2Discoverer.getDiscoverer(); + if (jws2servs != null) + { + if (jws2servs.hasServices()) + { + jws2servs.attachWSMenuEntry(webService, me); + for (Jws2Instance sv : jws2servs.getServices()) + { + if (sv.description.toLowerCase().contains("jpred")) + { + for (JMenuItem jmi : legacyItems) + { + jmi.setVisible(false); + } + } + } + + } + if (jws2servs.isRunning()) + { + JMenuItem tm = new JMenuItem( + "Still discovering JABA Services"); + tm.setEnabled(false); + webService.add(tm); + } + } + } + build_urlServiceMenu(me.webService); + build_fetchdbmenu(webService); + for (JMenu item : wsmenu) + { + if (item.getItemCount() == 0) + { + item.setEnabled(false); + } + else + { + item.setEnabled(true); + } + } + } catch (Exception e) + { + Cache.log + .debug("Exception during web service menu building process.", + e); + } + } + }); + } catch (Exception e) + { + } + buildingMenu = false; + } + }).start(); + + } + + /** + * construct any groupURL type service menu entries. + * + * @param webService + */ + private void build_urlServiceMenu(JMenu webService) + { + // TODO: remove this code when 2.7 is released + // DEBUG - alignmentView + /* + * JMenuItem testAlView = new JMenuItem("Test AlignmentView"); final + * AlignFrame af = this; testAlView.addActionListener(new ActionListener() { + * + * @Override public void actionPerformed(ActionEvent e) { + * jalview.datamodel.AlignmentView + * .testSelectionViews(af.viewport.getAlignment(), + * af.viewport.getColumnSelection(), af.viewport.selectionGroup); } + * + * }); webService.add(testAlView); + */ + // TODO: refactor to RestClient discoverer and merge menu entries for + // rest-style services with other types of analysis/calculation service + // SHmmr test client - still being implemented. + // DEBUG - alignmentView + + for (jalview.ws.rest.RestClient client : jalview.ws.rest.RestClient + .getRestClients()) + { + client.attachWSMenuEntry( + JvSwingUtils.findOrCreateMenu(webService, client.getAction()), + this); + } + } + + /** + * Searches selected sequences for xRef products and builds the Show + * Cross-References menu (formerly called Show Products) + * + * @return true if Show Cross-references menu should be enabled. + */ + public boolean canShowProducts() + { + SequenceI[] selection = viewport.getSequenceSelection(); + AlignmentI dataset = viewport.getAlignment().getDataset(); + boolean showp = false; + try + { + showProducts.removeAll(); + final boolean dna = viewport.getAlignment().isNucleotide(); + String[] ptypes = (selection == null || selection.length == 0) ? null + : CrossRef.findSequenceXrefTypes(dna, selection, dataset); + + for (int t = 0; ptypes != null && t < ptypes.length; t++) + { + showp = true; + final AlignFrame af = this; + final String source = ptypes[t]; + JMenuItem xtype = new JMenuItem(ptypes[t]); + xtype.addActionListener(new ActionListener() + { + + @Override + public void actionPerformed(ActionEvent e) + { + showProductsFor(af.viewport.getSequenceSelection(), dna, source); + } + + }); + showProducts.add(xtype); + } + showProducts.setVisible(showp); + showProducts.setEnabled(showp); + } catch (Exception e) + { + jalview.bin.Cache.log + .warn("canShowProducts threw an exception - please report to help@jalview.org", + e); + return false; + } + return showp; + } + + /** + * Finds and displays cross-references for the selected sequences (protein + * products for nucleotide sequences, dna coding sequences for peptides). + * + * @param sel + * the sequences to show cross-references for + * @param dna + * true if from a nucleotide alignment (so showing proteins) + * @param source + * the database to show cross-references for + */ + protected void showProductsFor(final SequenceI[] sel, final boolean dna, + final String source) + { + Runnable foo = new Runnable() + { + + @Override + public void run() + { + final long sttime = System.currentTimeMillis(); + AlignFrame.this.setProgressBar(MessageManager.formatMessage( + "status.searching_for_sequences_from", + new Object[] { source }), sttime); + try + { + AlignmentI alignment = AlignFrame.this.getViewport() + .getAlignment(); + AlignmentI xrefs = CrossRef.findXrefSequences(sel, dna, source, + alignment); + if (xrefs != null) + { + /* + * get display scheme (if any) to apply to features + */ + FeatureSettingsModelI featureColourScheme = new SequenceFetcher() + .getFeatureColourScheme(source); + + AlignmentI al = makeCrossReferencesAlignment( + alignment.getDataset(), xrefs); + + AlignFrame newFrame = new AlignFrame(al, DEFAULT_WIDTH, + DEFAULT_HEIGHT); + if (Cache.getDefault("HIDE_INTRONS", true)) + { + newFrame.hideFeatureColumns(SequenceOntologyI.EXON, false); + } + String newtitle = String.format("%s %s %s", + MessageManager.getString(dna ? "label.proteins" + : "label.nucleotides"), MessageManager + .getString("label.for"), getTitle()); + newFrame.setTitle(newtitle); + + if (!Cache.getDefault(Preferences.ENABLE_SPLIT_FRAME, true)) + { + /* + * split frame display is turned off in preferences file + */ + Desktop.addInternalFrame(newFrame, newtitle, DEFAULT_WIDTH, + DEFAULT_HEIGHT); + return; // via finally clause + } + + /* + * Make a copy of this alignment (sharing the same dataset + * sequences). If we are DNA, drop introns and update mappings + */ + AlignmentI copyAlignment = null; + final SequenceI[] sequenceSelection = AlignFrame.this.viewport + .getSequenceSelection(); + List cf = xrefs.getCodonFrames(); + boolean copyAlignmentIsAligned = false; + if (dna) + { + copyAlignment = AlignmentUtils.makeCdsAlignment( + sequenceSelection, cf, alignment); + if (copyAlignment.getHeight() == 0) + { + System.err.println("Failed to make CDS alignment"); + } + al.getCodonFrames().clear(); + al.addCodonFrames(copyAlignment.getCodonFrames()); + al.addCodonFrames(cf); + + /* + * pending getting Embl transcripts to 'align', + * we are only doing this for Ensembl + */ + // TODO proper criteria for 'can align as cdna' + if (DBRefSource.ENSEMBL.equalsIgnoreCase(source) + || AlignmentUtils.looksLikeEnsembl(alignment)) + { + copyAlignment.alignAs(alignment); + copyAlignmentIsAligned = true; + } + } + else + { + copyAlignment = AlignmentUtils.makeCopyAlignment( + sequenceSelection, xrefs.getSequencesArray()); + copyAlignment.addCodonFrames(cf); + al.addCodonFrames(copyAlignment.getCodonFrames()); + al.addCodonFrames(cf); + } + copyAlignment.setGapCharacter(AlignFrame.this.viewport + .getGapCharacter()); + + StructureSelectionManager ssm = StructureSelectionManager + .getStructureSelectionManager(Desktop.instance); + ssm.registerMappings(cf); + + if (copyAlignment.getHeight() <= 0) + { + System.err.println("No Sequences generated for xRef type " + + source); + return; + } + /* + * align protein to dna + */ + if (dna && copyAlignmentIsAligned) + { + al.alignAs(copyAlignment); + } + else + { + /* + * align cdna to protein - currently only if + * fetching and aligning Ensembl transcripts! + */ + if (DBRefSource.ENSEMBL.equalsIgnoreCase(source)) + { + copyAlignment.alignAs(al); + } + } + + AlignFrame copyThis = new AlignFrame(copyAlignment, + AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT); + copyThis.setTitle(AlignFrame.this.getTitle()); + + boolean showSequenceFeatures = viewport + .isShowSequenceFeatures(); + newFrame.setShowSeqFeatures(showSequenceFeatures); + copyThis.setShowSeqFeatures(showSequenceFeatures); + FeatureRenderer myFeatureStyling = alignPanel.getSeqPanel().seqCanvas + .getFeatureRenderer(); + + /* + * copy feature rendering settings to split frame + */ + newFrame.alignPanel.getSeqPanel().seqCanvas + .getFeatureRenderer() + .transferSettings(myFeatureStyling); + copyThis.alignPanel.getSeqPanel().seqCanvas + .getFeatureRenderer() + .transferSettings(myFeatureStyling); + + /* + * apply 'database source' feature configuration + * if any was found + */ + // TODO is this the feature colouring for the original + // alignment or the fetched xrefs? either could be Ensembl + newFrame.getViewport().applyFeaturesStyle(featureColourScheme); + copyThis.getViewport().applyFeaturesStyle(featureColourScheme); + + SplitFrame sf = new SplitFrame(dna ? copyThis : newFrame, + dna ? newFrame : copyThis); + newFrame.setVisible(true); + copyThis.setVisible(true); + String linkedTitle = MessageManager + .getString("label.linked_view_title"); + Desktop.addInternalFrame(sf, linkedTitle, -1, -1); + sf.adjustDivider(); + } + } catch (Exception e) + { + Cache.log.error("Exception when finding crossreferences", e); + } catch (OutOfMemoryError e) + { + new OOMWarning("whilst fetching crossreferences", e); + } catch (Throwable e) + { + Cache.log.error("Error when finding crossreferences", e); + } finally + { + AlignFrame.this.setProgressBar(MessageManager.formatMessage( + "status.finished_searching_for_sequences_from", + new Object[] { source }), sttime); + } + } + + /** + * Makes an alignment containing the given sequences. If this is of the + * same type as the given dataset (nucleotide/protein), then the new + * alignment shares the same dataset, and its dataset sequences are added + * to it. Otherwise a new dataset sequence is created for the + * cross-references. + * + * @param dataset + * @param seqs + * @return + */ + protected AlignmentI makeCrossReferencesAlignment(AlignmentI dataset, + AlignmentI seqs) + { + boolean sameType = dataset.isNucleotide() == seqs.isNucleotide(); + + SequenceI[] sprods = new SequenceI[seqs.getHeight()]; + for (int s = 0; s < sprods.length; s++) + { + sprods[s] = (seqs.getSequenceAt(s)).deriveSequence(); + if (sameType) + { + if (dataset.getSequences() == null + || !dataset.getSequences().contains( + sprods[s].getDatasetSequence())) + { + dataset.addSequence(sprods[s].getDatasetSequence()); + } + } + sprods[s].updatePDBIds(); + } + Alignment al = new Alignment(sprods); + if (sameType) + { + al.setDataset((Alignment) dataset); + } + else + { + al.createDatasetAlignment(); + } + return al; + } + + }; + Thread frunner = new Thread(foo); + frunner.start(); + } + + /** + * Construct and display a new frame containing the translation of this + * frame's DNA sequences to their aligned protein (amino acid) equivalents. + */ + @Override + public void showTranslation_actionPerformed(ActionEvent e) + { + AlignmentI al = null; + try + { + Dna dna = new Dna(viewport, viewport.getViewAsVisibleContigs(true)); + + al = dna.translateCdna(); + } catch (Exception ex) + { + jalview.bin.Cache.log.error( + "Exception during translation. Please report this !", ex); + final String msg = MessageManager + .getString("label.error_when_translating_sequences_submit_bug_report"); + final String errorTitle = MessageManager + .getString("label.implementation_error") + + MessageManager.getString("label.translation_failed"); + JOptionPane.showMessageDialog(Desktop.desktop, msg, errorTitle, + JOptionPane.ERROR_MESSAGE); + return; + } + if (al == null || al.getHeight() == 0) + { + final String msg = MessageManager + .getString("label.select_at_least_three_bases_in_at_least_one_sequence_to_cDNA_translation"); + final String errorTitle = MessageManager + .getString("label.translation_failed"); + JOptionPane.showMessageDialog(Desktop.desktop, msg, errorTitle, + JOptionPane.WARNING_MESSAGE); + } + else + { + AlignFrame af = new AlignFrame(al, DEFAULT_WIDTH, DEFAULT_HEIGHT); + af.setFileFormat(this.currentFileFormat); + final String newTitle = MessageManager.formatMessage( + "label.translation_of_params", + new Object[] { this.getTitle() }); + af.setTitle(newTitle); + if (Cache.getDefault(Preferences.ENABLE_SPLIT_FRAME, true)) + { + final SequenceI[] seqs = viewport.getSelectionAsNewSequence(); + viewport.openSplitFrame(af, new Alignment(seqs)); + } + else + { + Desktop.addInternalFrame(af, newTitle, DEFAULT_WIDTH, + DEFAULT_HEIGHT); + } + } + } + + /** + * Set the file format + * + * @param fileFormat + */ + public void setFileFormat(String fileFormat) + { + this.currentFileFormat = fileFormat; + } + + /** + * Try to load a features file onto the alignment. + * + * @param file + * contents or path to retrieve file + * @param type + * access mode of file (see jalview.io.AlignFile) + * @return true if features file was parsed correctly. + */ + public boolean parseFeaturesFile(String file, String type) + { + return avc.parseFeaturesFile(file, type, + jalview.bin.Cache.getDefault("RELAXEDSEQIDMATCHING", false)); + + } + + @Override + public void refreshFeatureUI(boolean enableIfNecessary) + { + // note - currently this is only still here rather than in the controller + // because of the featureSettings hard reference that is yet to be + // abstracted + if (enableIfNecessary) + { + viewport.setShowSequenceFeatures(true); + showSeqFeatures.setSelected(true); + } + + } + + @Override + public void dragEnter(DropTargetDragEvent evt) + { + } + + @Override + public void dragExit(DropTargetEvent evt) + { + } + + @Override + public void dragOver(DropTargetDragEvent evt) + { + } + + @Override + public void dropActionChanged(DropTargetDragEvent evt) + { + } + + @Override + public void drop(DropTargetDropEvent evt) + { + Transferable t = evt.getTransferable(); + java.util.List files = new ArrayList(), protocols = new ArrayList(); + + try + { + Desktop.transferFromDropTarget(files, protocols, evt, t); + } catch (Exception e) + { + e.printStackTrace(); + } + if (files != null) + { + try + { + // check to see if any of these files have names matching sequences in + // the alignment + SequenceIdMatcher idm = new SequenceIdMatcher(viewport + .getAlignment().getSequencesArray()); + /** + * Object[] { String,SequenceI} + */ + ArrayList filesmatched = new ArrayList(); + ArrayList filesnotmatched = new ArrayList(); + for (int i = 0; i < files.size(); i++) + { + String file = files.get(i).toString(); + String pdbfn = ""; + String protocol = FormatAdapter.checkProtocol(file); + if (protocol == jalview.io.FormatAdapter.FILE) + { + File fl = new File(file); + pdbfn = fl.getName(); + } + else if (protocol == jalview.io.FormatAdapter.URL) + { + URL url = new URL(file); + pdbfn = url.getFile(); + } + if (pdbfn.length() > 0) + { + // attempt to find a match in the alignment + SequenceI[] mtch = idm.findAllIdMatches(pdbfn); + int l = 0, c = pdbfn.indexOf("."); + while (mtch == null && c != -1) + { + do + { + l = c; + } while ((c = pdbfn.indexOf(".", l)) > l); + if (l > -1) + { + pdbfn = pdbfn.substring(0, l); + } + mtch = idm.findAllIdMatches(pdbfn); + } + if (mtch != null) + { + String type = null; + try + { + type = new IdentifyFile().identify(file, protocol); + } catch (Exception ex) + { + type = null; + } + if (type != null) + { + if (type.equalsIgnoreCase("PDB")) + { + filesmatched.add(new Object[] { file, protocol, mtch }); + continue; + } + } + } + // File wasn't named like one of the sequences or wasn't a PDB file. + filesnotmatched.add(file); + } + } + int assocfiles = 0; + if (filesmatched.size() > 0) + { + if (Cache.getDefault("AUTOASSOCIATE_PDBANDSEQS", false) + || JOptionPane + .showConfirmDialog( + this, + MessageManager + .formatMessage( + "label.automatically_associate_pdb_files_with_sequences_same_name", + new Object[] { Integer + .valueOf( + filesmatched + .size()) + .toString() }), + MessageManager + .getString("label.automatically_associate_pdb_files_by_name"), + JOptionPane.YES_NO_OPTION) == JOptionPane.YES_OPTION) + + { + for (Object[] fm : filesmatched) + { + // try and associate + // TODO: may want to set a standard ID naming formalism for + // associating PDB files which have no IDs. + for (SequenceI toassoc : (SequenceI[]) fm[2]) + { + PDBEntry pe = new AssociatePdbFileWithSeq() + .associatePdbWithSeq((String) fm[0], + (String) fm[1], toassoc, false, + Desktop.instance); + if (pe != null) + { + System.err.println("Associated file : " + + ((String) fm[0]) + " with " + + toassoc.getDisplayId(true)); + assocfiles++; + } + } + alignPanel.paintAlignment(true); + } + } + } + if (filesnotmatched.size() > 0) + { + if (assocfiles > 0 + && (Cache.getDefault( + "AUTOASSOCIATE_PDBANDSEQS_IGNOREOTHERS", false) || JOptionPane + .showConfirmDialog( + this, + "" + + MessageManager + .formatMessage( + "label.ignore_unmatched_dropped_files_info", + new Object[] { Integer + .valueOf( + filesnotmatched + .size()) + .toString() }) + + "", + MessageManager + .getString("label.ignore_unmatched_dropped_files"), + JOptionPane.YES_NO_OPTION) == JOptionPane.YES_OPTION)) + { + return; + } + for (String fn : filesnotmatched) + { + loadJalviewDataFile(fn, null, null, null); + } + + } + } catch (Exception ex) + { + ex.printStackTrace(); + } + } + } + + /** + * Attempt to load a "dropped" file or URL string: First by testing whether + * it's an Annotation file, then a JNet file, and finally a features file. If + * all are false then the user may have dropped an alignment file onto this + * AlignFrame. + * + * @param file + * either a filename or a URL string. + */ + public void loadJalviewDataFile(String file, String protocol, + String format, SequenceI assocSeq) + { + try + { + if (protocol == null) + { + protocol = FormatAdapter.checkProtocol(file); + } + // if the file isn't identified, or not positively identified as some + // other filetype (PFAM is default unidentified alignment file type) then + // try to parse as annotation. + boolean isAnnotation = (format == null || format + .equalsIgnoreCase("PFAM")) ? new AnnotationFile() + .annotateAlignmentView(viewport, file, protocol) : false; + + if (!isAnnotation) + { + // first see if its a T-COFFEE score file + TCoffeeScoreFile tcf = null; + try + { + tcf = new TCoffeeScoreFile(file, protocol); + if (tcf.isValid()) + { + if (tcf.annotateAlignment(viewport.getAlignment(), true)) + { + tcoffeeColour.setEnabled(true); + tcoffeeColour.setSelected(true); + changeColour(new TCoffeeColourScheme(viewport.getAlignment())); + isAnnotation = true; + statusBar + .setText(MessageManager + .getString("label.successfully_pasted_tcoffee_scores_to_alignment")); + } + else + { + // some problem - if no warning its probable that the ID matching + // process didn't work + JOptionPane + .showMessageDialog( + Desktop.desktop, + tcf.getWarningMessage() == null ? MessageManager + .getString("label.check_file_matches_sequence_ids_alignment") + : tcf.getWarningMessage(), + MessageManager + .getString("label.problem_reading_tcoffee_score_file"), + JOptionPane.WARNING_MESSAGE); + } + } + else + { + tcf = null; + } + } catch (Exception x) + { + Cache.log + .debug("Exception when processing data source as T-COFFEE score file", + x); + tcf = null; + } + if (tcf == null) + { + // try to see if its a JNet 'concise' style annotation file *before* + // we + // try to parse it as a features file + if (format == null) + { + format = new IdentifyFile().identify(file, protocol); + } + if (format.equalsIgnoreCase("JnetFile")) + { + jalview.io.JPredFile predictions = new jalview.io.JPredFile( + file, protocol); + new JnetAnnotationMaker(); + JnetAnnotationMaker.add_annotation(predictions, + viewport.getAlignment(), 0, false); + SequenceI repseq = viewport.getAlignment().getSequenceAt(0); + viewport.getAlignment().setSeqrep(repseq); + ColumnSelection cs = new ColumnSelection(); + cs.hideInsertionsFor(repseq); + viewport.setColumnSelection(cs); + isAnnotation = true; + } + else if (IdentifyFile.FeaturesFile.equals(format)) + { + if (parseFeaturesFile(file, protocol)) + { + alignPanel.paintAlignment(true); + } + } + else + { + new FileLoader().LoadFile(viewport, file, protocol, format); + } + } + } + if (isAnnotation) + { + + alignPanel.adjustAnnotationHeight(); + viewport.updateSequenceIdColours(); + buildSortByAnnotationScoresMenu(); + alignPanel.paintAlignment(true); + } + } catch (Exception ex) + { + ex.printStackTrace(); + } catch (OutOfMemoryError oom) + { + try + { + System.gc(); + } catch (Exception x) + { + } + new OOMWarning( + "loading data " + + (protocol != null ? (protocol.equals(FormatAdapter.PASTE) ? "from clipboard." + : "using " + protocol + " from " + file) + : ".") + + (format != null ? "(parsing as '" + format + + "' file)" : ""), oom, Desktop.desktop); + } + } + + /** + * Method invoked by the ChangeListener on the tabbed pane, in other words + * when a different tabbed pane is selected by the user or programmatically. + */ + @Override + public void tabSelectionChanged(int index) + { + if (index > -1) + { + alignPanel = alignPanels.get(index); + viewport = alignPanel.av; + avc.setViewportAndAlignmentPanel(viewport, alignPanel); + setMenusFromViewport(viewport); + } + + /* + * If there is a frame linked to this one in a SplitPane, switch it to the + * same view tab index. No infinite recursion of calls should happen, since + * tabSelectionChanged() should not get invoked on setting the selected + * index to an unchanged value. Guard against setting an invalid index + * before the new view peer tab has been created. + */ + final AlignViewportI peer = viewport.getCodingComplement(); + if (peer != null) + { + AlignFrame linkedAlignFrame = ((AlignViewport) peer).getAlignPanel().alignFrame; + if (linkedAlignFrame.tabbedPane.getTabCount() > index) + { + linkedAlignFrame.tabbedPane.setSelectedIndex(index); + } + } + } + + /** + * On right mouse click on view tab, prompt for and set new view name. + */ + @Override + public void tabbedPane_mousePressed(MouseEvent e) + { + if (e.isPopupTrigger()) + { + String msg = MessageManager.getString("label.enter_view_name"); + String reply = JOptionPane.showInternalInputDialog(this, msg, msg, + JOptionPane.QUESTION_MESSAGE); + + if (reply != null) + { + viewport.viewName = reply; + // TODO warn if reply is in getExistingViewNames()? + tabbedPane.setTitleAt(tabbedPane.getSelectedIndex(), reply); + } + } + } + + public AlignViewport getCurrentView() + { + return viewport; + } + + /** + * Open the dialog for regex description parsing. + */ + @Override + protected void extractScores_actionPerformed(ActionEvent e) + { + ParseProperties pp = new jalview.analysis.ParseProperties( + viewport.getAlignment()); + // TODO: verify regex and introduce GUI dialog for version 2.5 + // if (pp.getScoresFromDescription("col", "score column ", + // "\\W*([-+]?\\d*\\.?\\d*e?-?\\d*)\\W+([-+]?\\d*\\.?\\d*e?-?\\d*)", + // true)>0) + if (pp.getScoresFromDescription("description column", + "score in description column ", "\\W*([-+eE0-9.]+)", true) > 0) + { + buildSortByAnnotationScoresMenu(); + } + } + + /* + * (non-Javadoc) + * + * @see + * jalview.jbgui.GAlignFrame#showDbRefs_actionPerformed(java.awt.event.ActionEvent + * ) + */ + @Override + protected void showDbRefs_actionPerformed(ActionEvent e) + { + viewport.setShowDBRefs(showDbRefsMenuitem.isSelected()); + } + + /* + * (non-Javadoc) + * + * @seejalview.jbgui.GAlignFrame#showNpFeats_actionPerformed(java.awt.event. + * ActionEvent) + */ + @Override + protected void showNpFeats_actionPerformed(ActionEvent e) + { + viewport.setShowNPFeats(showNpFeatsMenuitem.isSelected()); + } + + /** + * find the viewport amongst the tabs in this alignment frame and close that + * tab + * + * @param av + */ + public boolean closeView(AlignViewportI av) + { + if (viewport == av) + { + this.closeMenuItem_actionPerformed(false); + return true; + } + Component[] comp = tabbedPane.getComponents(); + for (int i = 0; comp != null && i < comp.length; i++) + { + if (comp[i] instanceof AlignmentPanel) + { + if (((AlignmentPanel) comp[i]).av == av) + { + // close the view. + closeView((AlignmentPanel) comp[i]); + return true; + } + } + } + return false; + } + + protected void build_fetchdbmenu(JMenu webService) + { + // Temporary hack - DBRef Fetcher always top level ws entry. + // TODO We probably want to store a sequence database checklist in + // preferences and have checkboxes.. rather than individual sources selected + // here + final JMenu rfetch = new JMenu( + MessageManager.getString("action.fetch_db_references")); + rfetch.setToolTipText(MessageManager + .getString("label.retrieve_parse_sequence_database_records_alignment_or_selected_sequences")); + webService.add(rfetch); + + final JCheckBoxMenuItem trimrs = new JCheckBoxMenuItem( + MessageManager.getString("option.trim_retrieved_seqs")); + trimrs.setToolTipText(MessageManager + .getString("label.trim_retrieved_sequences")); + trimrs.setSelected(Cache.getDefault("TRIM_FETCHED_DATASET_SEQS", true)); + trimrs.addActionListener(new ActionListener() + { + @Override + public void actionPerformed(ActionEvent e) + { + trimrs.setSelected(trimrs.isSelected()); + Cache.setProperty("TRIM_FETCHED_DATASET_SEQS", + Boolean.valueOf(trimrs.isSelected()).toString()); + }; + }); + rfetch.add(trimrs); + JMenuItem fetchr = new JMenuItem( + MessageManager.getString("label.standard_databases")); + fetchr.setToolTipText(MessageManager + .getString("label.fetch_embl_uniprot")); + fetchr.addActionListener(new ActionListener() + { + + @Override + public void actionPerformed(ActionEvent e) + { + new Thread(new Runnable() + { + @Override + public void run() + { + boolean isNucleotide = alignPanel.alignFrame.getViewport() + .getAlignment().isNucleotide(); + DBRefFetcher dbRefFetcher = new DBRefFetcher(alignPanel.av + .getSequenceSelection(), alignPanel.alignFrame, null, + alignPanel.alignFrame.featureSettings, isNucleotide); + dbRefFetcher.addListener(new FetchFinishedListenerI() + { + @Override + public void finished() + { + AlignFrame.this.setMenusForViewport(); + } + }); + dbRefFetcher.fetchDBRefs(false); + } + }).start(); + + } + + }); + rfetch.add(fetchr); + final AlignFrame me = this; + new Thread(new Runnable() + { + @Override + public void run() + { + final jalview.ws.SequenceFetcher sf = jalview.gui.SequenceFetcher + .getSequenceFetcherSingleton(me); + javax.swing.SwingUtilities.invokeLater(new Runnable() + { + @Override + public void run() + { + String[] dbclasses = sf.getOrderedSupportedSources(); + // sf.getDbInstances(jalview.ws.dbsources.DasSequenceSource.class); + // jalview.util.QuickSort.sort(otherdb, otherdb); + List otherdb; + JMenu dfetch = new JMenu(); + JMenu ifetch = new JMenu(); + JMenuItem fetchr = null; + int comp = 0, icomp = 0, mcomp = 15; + String mname = null; + int dbi = 0; + for (String dbclass : dbclasses) + { + otherdb = sf.getSourceProxy(dbclass); + // add a single entry for this class, or submenu allowing 'fetch + // all' or pick one + if (otherdb == null || otherdb.size() < 1) + { + continue; + } + // List dbs=otherdb; + // otherdb=new ArrayList(); + // for (DbSourceProxy db:dbs) + // { + // if (!db.isA(DBRefSource.ALIGNMENTDB) + // } + if (mname == null) + { + mname = "From " + dbclass; + } + if (otherdb.size() == 1) + { + final DbSourceProxy[] dassource = otherdb + .toArray(new DbSourceProxy[0]); + DbSourceProxy src = otherdb.get(0); + fetchr = new JMenuItem(src.getDbSource()); + fetchr.addActionListener(new ActionListener() + { + + @Override + public void actionPerformed(ActionEvent e) + { + new Thread(new Runnable() + { + + @Override + public void run() + { + boolean isNucleotide = alignPanel.alignFrame + .getViewport().getAlignment() + .isNucleotide(); + DBRefFetcher dbRefFetcher = new DBRefFetcher( + alignPanel.av.getSequenceSelection(), + alignPanel.alignFrame, dassource, + alignPanel.alignFrame.featureSettings, + isNucleotide); + dbRefFetcher + .addListener(new FetchFinishedListenerI() + { + @Override + public void finished() + { + AlignFrame.this.setMenusForViewport(); + } + }); + dbRefFetcher.fetchDBRefs(false); + } + }).start(); + } + + }); + fetchr.setToolTipText(JvSwingUtils.wrapTooltip(true, + MessageManager.formatMessage( + "label.fetch_retrieve_from", + new Object[] { src.getDbName() }))); + dfetch.add(fetchr); + comp++; + } + else + { + final DbSourceProxy[] dassource = otherdb + .toArray(new DbSourceProxy[0]); + // fetch all entry + DbSourceProxy src = otherdb.get(0); + fetchr = new JMenuItem(MessageManager.formatMessage( + "label.fetch_all_param", + new Object[] { src.getDbSource() })); + fetchr.addActionListener(new ActionListener() + { + @Override + public void actionPerformed(ActionEvent e) + { + new Thread(new Runnable() + { + + @Override + public void run() + { + boolean isNucleotide = alignPanel.alignFrame + .getViewport().getAlignment() + .isNucleotide(); + DBRefFetcher dbRefFetcher = new DBRefFetcher( + alignPanel.av.getSequenceSelection(), + alignPanel.alignFrame, dassource, + alignPanel.alignFrame.featureSettings, + isNucleotide); + dbRefFetcher + .addListener(new FetchFinishedListenerI() + { + @Override + public void finished() + { + AlignFrame.this.setMenusForViewport(); + } + }); + dbRefFetcher.fetchDBRefs(false); + } + }).start(); + } + }); + + fetchr.setToolTipText(JvSwingUtils.wrapTooltip(true, + MessageManager.formatMessage( + "label.fetch_retrieve_from_all_sources", + new Object[] { + Integer.valueOf(otherdb.size()) + .toString(), src.getDbSource(), + src.getDbName() }))); + dfetch.add(fetchr); + comp++; + // and then build the rest of the individual menus + ifetch = new JMenu(MessageManager.formatMessage( + "label.source_from_db_source", + new Object[] { src.getDbSource() })); + icomp = 0; + String imname = null; + int i = 0; + for (DbSourceProxy sproxy : otherdb) + { + String dbname = sproxy.getDbName(); + String sname = dbname.length() > 5 ? dbname.substring(0, + 5) + "..." : dbname; + String msname = dbname.length() > 10 ? dbname.substring( + 0, 10) + "..." : dbname; + if (imname == null) + { + imname = MessageManager.formatMessage( + "label.from_msname", new Object[] { sname }); + } + fetchr = new JMenuItem(msname); + final DbSourceProxy[] dassrc = { sproxy }; + fetchr.addActionListener(new ActionListener() + { + + @Override + public void actionPerformed(ActionEvent e) + { + new Thread(new Runnable() + { + + @Override + public void run() + { + boolean isNucleotide = alignPanel.alignFrame + .getViewport().getAlignment() + .isNucleotide(); + DBRefFetcher dbRefFetcher = new DBRefFetcher( + alignPanel.av.getSequenceSelection(), + alignPanel.alignFrame, dassrc, + alignPanel.alignFrame.featureSettings, + isNucleotide); + dbRefFetcher + .addListener(new FetchFinishedListenerI() + { + @Override + public void finished() + { + AlignFrame.this.setMenusForViewport(); + } + }); + dbRefFetcher.fetchDBRefs(false); + } + }).start(); + } + + }); + fetchr.setToolTipText("" + + MessageManager.formatMessage( + "label.fetch_retrieve_from", new Object[] + { dbname })); + ifetch.add(fetchr); + ++i; + if (++icomp >= mcomp || i == (otherdb.size())) + { + ifetch.setText(MessageManager.formatMessage( + "label.source_to_target", imname, sname)); + dfetch.add(ifetch); + ifetch = new JMenu(); + imname = null; + icomp = 0; + comp++; + } + } + } + ++dbi; + if (comp >= mcomp || dbi >= (dbclasses.length)) + { + dfetch.setText(MessageManager.formatMessage( + "label.source_to_target", mname, dbclass)); + rfetch.add(dfetch); + dfetch = new JMenu(); + mname = null; + comp = 0; + } + } + } + }); + } + }).start(); + + } + + /** + * Left justify the whole alignment. + */ + @Override + protected void justifyLeftMenuItem_actionPerformed(ActionEvent e) + { + AlignmentI al = viewport.getAlignment(); + al.justify(false); + viewport.firePropertyChange("alignment", null, al); + } + + /** + * Right justify the whole alignment. + */ + @Override + protected void justifyRightMenuItem_actionPerformed(ActionEvent e) + { + AlignmentI al = viewport.getAlignment(); + al.justify(true); + viewport.firePropertyChange("alignment", null, al); + } + + @Override + public void setShowSeqFeatures(boolean b) + { + showSeqFeatures.setSelected(b); + viewport.setShowSequenceFeatures(b); + } + + /* + * (non-Javadoc) + * + * @see + * jalview.jbgui.GAlignFrame#showUnconservedMenuItem_actionPerformed(java. + * awt.event.ActionEvent) + */ + @Override + protected void showUnconservedMenuItem_actionPerformed(ActionEvent e) + { + viewport.setShowUnconserved(showNonconservedMenuItem.getState()); + alignPanel.paintAlignment(true); + } + + /* + * (non-Javadoc) + * + * @see + * jalview.jbgui.GAlignFrame#showGroupConsensus_actionPerformed(java.awt.event + * .ActionEvent) + */ + @Override + protected void showGroupConsensus_actionPerformed(ActionEvent e) + { + viewport.setShowGroupConsensus(showGroupConsensus.getState()); + alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState()); + + } + + /* + * (non-Javadoc) + * + * @see + * jalview.jbgui.GAlignFrame#showGroupConservation_actionPerformed(java.awt + * .event.ActionEvent) + */ + @Override + protected void showGroupConservation_actionPerformed(ActionEvent e) + { + viewport.setShowGroupConservation(showGroupConservation.getState()); + alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState()); + } + + /* + * (non-Javadoc) + * + * @see + * jalview.jbgui.GAlignFrame#showConsensusHistogram_actionPerformed(java.awt + * .event.ActionEvent) + */ + @Override + protected void showConsensusHistogram_actionPerformed(ActionEvent e) + { + viewport.setShowConsensusHistogram(showConsensusHistogram.getState()); + alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState()); + } + + /* + * (non-Javadoc) + * + * @see + * jalview.jbgui.GAlignFrame#showConsensusProfile_actionPerformed(java.awt + * .event.ActionEvent) + */ + @Override + protected void showSequenceLogo_actionPerformed(ActionEvent e) + { + viewport.setShowSequenceLogo(showSequenceLogo.getState()); + alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState()); + } + + @Override + protected void normaliseSequenceLogo_actionPerformed(ActionEvent e) + { + showSequenceLogo.setState(true); + viewport.setShowSequenceLogo(true); + viewport.setNormaliseSequenceLogo(normaliseSequenceLogo.getState()); + alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState()); + } + + @Override + protected void applyAutoAnnotationSettings_actionPerformed(ActionEvent e) + { + alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState()); + } + + /* + * (non-Javadoc) + * + * @see + * jalview.jbgui.GAlignFrame#makeGrpsFromSelection_actionPerformed(java.awt + * .event.ActionEvent) + */ + @Override + protected void makeGrpsFromSelection_actionPerformed(ActionEvent e) + { + if (avc.makeGroupsFromSelection()) + { + PaintRefresher.Refresh(this, viewport.getSequenceSetId()); + alignPanel.updateAnnotation(); + alignPanel.paintAlignment(true); + } + } + + public void clearAlignmentSeqRep() + { + // TODO refactor alignmentseqrep to controller + if (viewport.getAlignment().hasSeqrep()) + { + viewport.getAlignment().setSeqrep(null); + PaintRefresher.Refresh(this, viewport.getSequenceSetId()); + alignPanel.updateAnnotation(); + alignPanel.paintAlignment(true); + } + } + + @Override + protected void createGroup_actionPerformed(ActionEvent e) + { + if (avc.createGroup()) + { + alignPanel.alignmentChanged(); + } + } + + @Override + protected void unGroup_actionPerformed(ActionEvent e) + { + if (avc.unGroup()) + { + alignPanel.alignmentChanged(); + } + } + + /** + * make the given alignmentPanel the currently selected tab + * + * @param alignmentPanel + */ + public void setDisplayedView(AlignmentPanel alignmentPanel) + { + if (!viewport.getSequenceSetId().equals( + alignmentPanel.av.getSequenceSetId())) + { + throw new Error( + MessageManager + .getString("error.implementation_error_cannot_show_view_alignment_frame")); + } + if (tabbedPane != null + && tabbedPane.getTabCount() > 0 + && alignPanels.indexOf(alignmentPanel) != tabbedPane + .getSelectedIndex()) + { + tabbedPane.setSelectedIndex(alignPanels.indexOf(alignmentPanel)); + } + } + + /** + * Action on selection of menu options to Show or Hide annotations. + * + * @param visible + * @param forSequences + * update sequence-related annotations + * @param forAlignment + * update non-sequence-related annotations + */ + @Override + protected void setAnnotationsVisibility(boolean visible, + boolean forSequences, boolean forAlignment) + { + for (AlignmentAnnotation aa : alignPanel.getAlignment() + .getAlignmentAnnotation()) + { + /* + * don't display non-positional annotations on an alignment + */ + if (aa.annotations == null) + { + continue; + } + boolean apply = (aa.sequenceRef == null && forAlignment) + || (aa.sequenceRef != null && forSequences); + if (apply) + { + aa.visible = visible; + } + } + alignPanel.validateAnnotationDimensions(true); + alignPanel.alignmentChanged(); + } + + /** + * Store selected annotation sort order for the view and repaint. + */ + @Override + protected void sortAnnotations_actionPerformed() + { + this.alignPanel.av.setSortAnnotationsBy(getAnnotationSortOrder()); + this.alignPanel.av + .setShowAutocalculatedAbove(isShowAutoCalculatedAbove()); + alignPanel.paintAlignment(true); + } + + /** + * + * @return alignment panels in this alignment frame + */ + public List getAlignPanels() + { + return alignPanels == null ? Arrays.asList(alignPanel) : alignPanels; + } + + /** + * Open a new alignment window, with the cDNA associated with this (protein) + * alignment, aligned as is the protein. + */ + protected void viewAsCdna_actionPerformed() + { + // TODO no longer a menu action - refactor as required + final AlignmentI alignment = getViewport().getAlignment(); + List mappings = alignment.getCodonFrames(); + if (mappings == null) + { + return; + } + List cdnaSeqs = new ArrayList(); + for (SequenceI aaSeq : alignment.getSequences()) + { + for (AlignedCodonFrame acf : mappings) + { + SequenceI dnaSeq = acf.getDnaForAaSeq(aaSeq.getDatasetSequence()); + if (dnaSeq != null) + { + /* + * There is a cDNA mapping for this protein sequence - add to new + * alignment. It will share the same dataset sequence as other mapped + * cDNA (no new mappings need to be created). + */ + final Sequence newSeq = new Sequence(dnaSeq); + newSeq.setDatasetSequence(dnaSeq); + cdnaSeqs.add(newSeq); + } + } + } + if (cdnaSeqs.size() == 0) + { + // show a warning dialog no mapped cDNA + return; + } + AlignmentI cdna = new Alignment(cdnaSeqs.toArray(new SequenceI[cdnaSeqs + .size()])); + AlignFrame alignFrame = new AlignFrame(cdna, AlignFrame.DEFAULT_WIDTH, + AlignFrame.DEFAULT_HEIGHT); + cdna.alignAs(alignment); + String newtitle = "cDNA " + MessageManager.getString("label.for") + " " + + this.title; + Desktop.addInternalFrame(alignFrame, newtitle, + AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT); + } + + /** + * Set visibility of dna/protein complement view (available when shown in a + * split frame). + * + * @param show + */ + @Override + protected void showComplement_actionPerformed(boolean show) + { + SplitContainerI sf = getSplitViewContainer(); + if (sf != null) + { + sf.setComplementVisible(this, show); + } + } + + /** + * Generate the reverse (optionally complemented) of the selected sequences, + * and add them to the alignment + */ + @Override + protected void showReverse_actionPerformed(boolean complement) + { + AlignmentI al = null; + try + { + Dna dna = new Dna(viewport, viewport.getViewAsVisibleContigs(true)); + al = dna.reverseCdna(complement); + viewport.addAlignment(al, ""); + addHistoryItem(new EditCommand( + MessageManager.getString("label.add_sequences"), + Action.PASTE, al.getSequencesArray(), 0, al.getWidth(), + viewport.getAlignment())); + } catch (Exception ex) + { + System.err.println(ex.getMessage()); + return; + } + } + + /** + * Try to run a script in the Groovy console, having first ensured that this + * AlignFrame is set as currentAlignFrame in Desktop, to allow the script to + * be targeted at this alignment. + */ + @Override + protected void runGroovy_actionPerformed() + { + Jalview.setCurrentAlignFrame(this); + groovy.ui.Console console = Desktop.getGroovyConsole(); + if (console != null) + { + try + { + console.runScript(); + } catch (Exception ex) + { + System.err.println((ex.toString())); + JOptionPane + .showInternalMessageDialog(Desktop.desktop, MessageManager + .getString("label.couldnt_run_groovy_script"), + MessageManager + .getString("label.groovy_support_failed"), + JOptionPane.ERROR_MESSAGE); + } + } + else + { + System.err.println("Can't run Groovy script as console not found"); + } + } + + /** + * Hides columns containing (or not containing) a specified feature, provided + * that would not leave all columns hidden + * + * @param featureType + * @param columnsContaining + * @return + */ + public boolean hideFeatureColumns(String featureType, + boolean columnsContaining) + { + boolean notForHiding = avc.markColumnsContainingFeatures( + columnsContaining, false, false, featureType); + if (notForHiding) + { + if (avc.markColumnsContainingFeatures(!columnsContaining, false, + false, featureType)) + { + getViewport().hideSelectedColumns(); + return true; + } + } + return false; + } +} + +class PrintThread extends Thread +{ + AlignmentPanel ap; + + public PrintThread(AlignmentPanel ap) + { + this.ap = ap; + } + + static PageFormat pf; + + @Override + public void run() + { + PrinterJob printJob = PrinterJob.getPrinterJob(); + + if (pf != null) + { + printJob.setPrintable(ap, pf); + } + else + { + printJob.setPrintable(ap); + } + + if (printJob.printDialog()) + { + try + { + printJob.print(); + } catch (Exception PrintException) + { + PrintException.printStackTrace(); + } + } + } +}