X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignFrame.java;h=9b91255f50ba15bc43994c328c9457f6738509c0;hb=797df64fa2a0a30773d0f48f5494d4155e5a8be3;hp=6302efb2456be83bebc9d3c180a4e8e9ad23569e;hpb=25eb28b39b04e155bb1157cb78efcd872a77058a;p=jalview.git diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java index 6302efb..9b91255 100755 --- a/src/jalview/gui/AlignFrame.java +++ b/src/jalview/gui/AlignFrame.java @@ -1,95 +1,258 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer - * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle - * - * This program is free software; you can redistribute it and/or - * modify it under the terms of the GNU General Public License - * as published by the Free Software Foundation; either version 2 - * of the License, or (at your option) any later version. - * - * This program is distributed in the hope that it will be useful, - * but WITHOUT ANY WARRANTY; without even the implied warranty of - * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the - * GNU General Public License for more details. - * - * You should have received a copy of the GNU General Public License - * along with this program; if not, write to the Free Softwarechang - * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7) + * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle + * + * This file is part of Jalview. + * + * Jalview is free software: you can redistribute it and/or + * modify it under the terms of the GNU General Public License + * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. + * + * Jalview is distributed in the hope that it will be useful, but + * WITHOUT ANY WARRANTY; without even the implied warranty + * of MERCHANTABILITY or FITNESS FOR A PARTICULAR + * PURPOSE. See the GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License along with Jalview. If not, see . */ package jalview.gui; -import java.beans.*; -import java.io.*; -import java.util.*; - -import java.awt.*; -import java.awt.datatransfer.*; -import java.awt.dnd.*; -import java.awt.event.*; -import java.awt.print.*; -import javax.swing.*; -import javax.swing.event.MenuEvent; - -import jalview.analysis.*; -import jalview.commands.*; -import jalview.datamodel.*; -import jalview.io.*; -import jalview.jbgui.*; -import jalview.schemes.*; -import jalview.ws.*; +import jalview.analysis.AAFrequency; +import jalview.analysis.AlignmentSorter; +import jalview.analysis.Conservation; +import jalview.analysis.CrossRef; +import jalview.analysis.NJTree; +import jalview.analysis.ParseProperties; +import jalview.analysis.SequenceIdMatcher; +import jalview.bin.Cache; +import jalview.commands.CommandI; +import jalview.commands.EditCommand; +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.AlignmentI; +import jalview.datamodel.AlignmentOrder; +import jalview.datamodel.AlignmentView; +import jalview.datamodel.ColumnSelection; +import jalview.datamodel.PDBEntry; +import jalview.datamodel.SeqCigar; +import jalview.datamodel.Sequence; +import jalview.datamodel.SequenceGroup; +import jalview.datamodel.SequenceI; +import jalview.io.AlignmentProperties; +import jalview.io.AnnotationFile; +import jalview.io.FeaturesFile; +import jalview.io.FileLoader; +import jalview.io.FormatAdapter; +import jalview.io.HTMLOutput; +import jalview.io.IdentifyFile; +import jalview.io.JalviewFileChooser; +import jalview.io.JalviewFileView; +import jalview.io.JnetAnnotationMaker; +import jalview.io.NewickFile; +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.ResidueProperties; +import jalview.schemes.StrandColourScheme; +import jalview.schemes.TaylorColourScheme; +import jalview.schemes.TurnColourScheme; +import jalview.schemes.UserColourScheme; +import jalview.schemes.ZappoColourScheme; +import jalview.ws.WSMenuEntryProviderI; +import jalview.ws.jws1.Discoverer; +import jalview.ws.jws2.Jws2Discoverer; + +import java.awt.BorderLayout; +import java.awt.Color; +import java.awt.Component; +import java.awt.GridLayout; +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.DnDConstants; +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.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.Enumeration; +import java.util.Hashtable; +import java.util.Vector; + +import javax.swing.JButton; +import javax.swing.JEditorPane; +import javax.swing.JInternalFrame; +import javax.swing.JLabel; +import javax.swing.JLayeredPane; +import javax.swing.JMenu; +import javax.swing.JMenuItem; +import javax.swing.JOptionPane; +import javax.swing.JPanel; +import javax.swing.JProgressBar; +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 +public class AlignFrame extends GAlignFrame implements DropTargetListener, + IProgressIndicator { + /** DOCUMENT ME!! */ public static final int DEFAULT_WIDTH = 700; /** DOCUMENT ME!! */ public static final int DEFAULT_HEIGHT = 500; + public AlignmentPanel alignPanel; AlignViewport viewport; Vector alignPanels = new Vector(); - - /** DOCUMENT ME!! */ + /** + * 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. - * - * @param al DOCUMENT ME! + * 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 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) + int width, int height, String sequenceSetId) { - this.setSize(width, height); - viewport = new AlignViewport(al, hiddenColumns); + 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); + viewport = new AlignViewport(al, hiddenColumns, sequenceSetId, viewId); alignPanel = new AlignmentPanel(this, viewport); - if(al.getDataset()==null) + if (al.getDataset() == null) { al.setDataset(null); } @@ -100,8 +263,11 @@ public class AlignFrame /** * Make a new AlignFrame from exisiting alignmentPanels - * @param ap AlignmentPanel - * @param av AlignViewport + * + * @param ap + * AlignmentPanel + * @param av + * AlignViewport */ public AlignFrame(AlignmentPanel ap) { @@ -111,6 +277,10 @@ public class AlignFrame init(); } + /** + * initalise the alignframe from the underlying viewport data and the + * configurations + */ void init() { if (viewport.conservation == null) @@ -118,12 +288,13 @@ public class AlignFrame BLOSUM62Colour.setEnabled(false); conservationMenuItem.setEnabled(false); modifyConservation.setEnabled(false); - // PIDColour.setEnabled(false); - // abovePIDThreshold.setEnabled(false); - // modifyPID.setEnabled(false); + // PIDColour.setEnabled(false); + // abovePIDThreshold.setEnabled(false); + // modifyPID.setEnabled(false); } - String sortby = jalview.bin.Cache.getDefault("SORT_ALIGNMENT", "No sort"); + String sortby = jalview.bin.Cache.getDefault("SORT_ALIGNMENT", + "No sort"); if (sortby.equals("Id")) { @@ -135,274 +306,253 @@ public class AlignFrame } if (Desktop.desktop != null) - { - this.setDropTarget(new java.awt.dnd.DropTarget(this, this)); - addServiceListeners(); - setGUINucleotide(viewport.alignment.isNucleotide()); - } + { + this.setDropTarget(new java.awt.dnd.DropTarget(this, this)); + addServiceListeners(); + setGUINucleotide(viewport.alignment.isNucleotide()); + } - setMenusFromViewport(viewport); - buildSortByAnnotationScoresMenu(); - if (viewport.wrapAlignment) - { - wrapMenuItem_actionPerformed(null); - } + setMenusFromViewport(viewport); + buildSortByAnnotationScoresMenu(); + if (viewport.wrapAlignment) + { + wrapMenuItem_actionPerformed(null); + } - if (jalview.bin.Cache.getDefault("SHOW_OVERVIEW",false)) + if (jalview.bin.Cache.getDefault("SHOW_OVERVIEW", false)) { this.overviewMenuItem_actionPerformed(null); } - addKeyListener(); + addKeyListener(); } + /** + * 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; - currentFileFormat = format; - reload.setEnabled(true); + fileName = file; + currentFileFormat = format; + reload.setEnabled(true); } void addKeyListener() { - addKeyListener(new KeyAdapter() + addKeyListener(new KeyAdapter() + { + public void keyPressed(KeyEvent evt) { - public void keyPressed(KeyEvent evt) + if (viewport.cursorMode + && ((evt.getKeyCode() >= KeyEvent.VK_0 && evt.getKeyCode() <= KeyEvent.VK_9) || (evt + .getKeyCode() >= KeyEvent.VK_NUMPAD0 && evt + .getKeyCode() <= KeyEvent.VK_NUMPAD9)) + && Character.isDigit(evt.getKeyChar())) + alignPanel.seqPanel.numberPressed(evt.getKeyChar()); + + switch (evt.getKeyCode()) { - if (viewport.cursorMode && - ( (evt.getKeyCode() >= KeyEvent.VK_0 && - evt.getKeyCode() <= KeyEvent.VK_9) - || - (evt.getKeyCode() >= KeyEvent.VK_NUMPAD0 && - evt.getKeyCode() <= KeyEvent.VK_NUMPAD9) - ) - && Character.isDigit(evt.getKeyChar())) - alignPanel.seqPanel.numberPressed(evt.getKeyChar()); - - switch (evt.getKeyCode()) - { - - case 27: // escape key - deselectAllSequenceMenuItem_actionPerformed(null); - break; + case 27: // escape key + deselectAllSequenceMenuItem_actionPerformed(null); - case KeyEvent.VK_DOWN: - if (evt.isAltDown() || !viewport.cursorMode) - moveSelectedSequences(false); - if (viewport.cursorMode) - alignPanel.seqPanel.moveCursor(0, 1); - break; + break; - case KeyEvent.VK_UP: - if (evt.isAltDown() || !viewport.cursorMode) - moveSelectedSequences(true); - if (viewport.cursorMode) - alignPanel.seqPanel.moveCursor(0, -1); + case KeyEvent.VK_DOWN: + if (evt.isAltDown() || !viewport.cursorMode) + moveSelectedSequences(false); + if (viewport.cursorMode) + alignPanel.seqPanel.moveCursor(0, 1); + break; - break; - - case KeyEvent.VK_LEFT: - if (evt.isAltDown() || !viewport.cursorMode) - slideSequences(false, - alignPanel.seqPanel.getKeyboardNo1()); - else - alignPanel.seqPanel.moveCursor( -1, 0); + case KeyEvent.VK_UP: + if (evt.isAltDown() || !viewport.cursorMode) + moveSelectedSequences(true); + if (viewport.cursorMode) + alignPanel.seqPanel.moveCursor(0, -1); + break; - break; + case KeyEvent.VK_LEFT: + if (evt.isAltDown() || !viewport.cursorMode) + slideSequences(false, alignPanel.seqPanel.getKeyboardNo1()); + else + alignPanel.seqPanel.moveCursor(-1, 0); - case KeyEvent.VK_RIGHT: - if (evt.isAltDown() || !viewport.cursorMode) - slideSequences(true, - alignPanel.seqPanel.getKeyboardNo1()); - else - alignPanel.seqPanel.moveCursor(1, 0); - break; + break; - case KeyEvent.VK_SPACE: - if (viewport.cursorMode) - { - alignPanel.seqPanel.insertGapAtCursor(evt.isControlDown() - || evt.isShiftDown() - || evt.isAltDown()); - } - break; + case KeyEvent.VK_RIGHT: + if (evt.isAltDown() || !viewport.cursorMode) + slideSequences(true, alignPanel.seqPanel.getKeyboardNo1()); + else + alignPanel.seqPanel.moveCursor(1, 0); + break; - case KeyEvent.VK_DELETE: - case KeyEvent.VK_BACK_SPACE: - if (!viewport.cursorMode) - { - cut_actionPerformed(null); - } - else + case KeyEvent.VK_SPACE: + if (viewport.cursorMode) + { + alignPanel.seqPanel.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) { - alignPanel.seqPanel.deleteGapAtCursor(evt.isControlDown() - || evt.isShiftDown() - || evt.isAltDown()); + System.out.println("closing bracket"); } + break; + */ + case KeyEvent.VK_DELETE: + case KeyEvent.VK_BACK_SPACE: + if (!viewport.cursorMode) + { + cut_actionPerformed(null); + } + else + { + alignPanel.seqPanel.deleteGapAtCursor(evt.isControlDown() + || evt.isShiftDown() || evt.isAltDown()); + } - break; - - case KeyEvent.VK_S: - if (viewport.cursorMode) - { - alignPanel.seqPanel.setCursorRow(); - } - break; - case KeyEvent.VK_C: - if (viewport.cursorMode && !evt.isControlDown()) - { - alignPanel.seqPanel.setCursorColumn(); - } - break; - case KeyEvent.VK_P: - if (viewport.cursorMode) - { - alignPanel.seqPanel.setCursorPosition(); - } - break; - - case KeyEvent.VK_ENTER: - case KeyEvent.VK_COMMA: - if (viewport.cursorMode) - { - alignPanel.seqPanel.setCursorRowAndColumn(); - } - break; - - case KeyEvent.VK_Q: - if (viewport.cursorMode) - { - alignPanel.seqPanel.setSelectionAreaAtCursor(true); - } - break; - case KeyEvent.VK_M: - if (viewport.cursorMode) - { - alignPanel.seqPanel.setSelectionAreaAtCursor(false); - } - break; - - case KeyEvent.VK_F2: - viewport.cursorMode = !viewport.cursorMode; - statusBar.setText("Keyboard editing mode is " + - (viewport.cursorMode ? "on" : "off")); - if (viewport.cursorMode) - { - alignPanel.seqPanel.seqCanvas.cursorX = viewport.startRes; - alignPanel.seqPanel.seqCanvas.cursorY = viewport.startSeq; - } - alignPanel.seqPanel.seqCanvas.repaint(); - break; + break; - case KeyEvent.VK_F1: - try - { - ClassLoader cl = jalview.gui.Desktop.class.getClassLoader(); - java.net.URL url = javax.help.HelpSet.findHelpSet(cl, "help/help"); - javax.help.HelpSet hs = new javax.help.HelpSet(cl, url); + case KeyEvent.VK_S: + if (viewport.cursorMode) + { + alignPanel.seqPanel.setCursorRow(); + } + break; + case KeyEvent.VK_C: + if (viewport.cursorMode && !evt.isControlDown()) + { + alignPanel.seqPanel.setCursorColumn(); + } + break; + case KeyEvent.VK_P: + if (viewport.cursorMode) + { + alignPanel.seqPanel.setCursorPosition(); + } + break; - javax.help.HelpBroker hb = hs.createHelpBroker(); - hb.setCurrentID("home"); - hb.setDisplayed(true); - } - catch (Exception ex) - { - ex.printStackTrace(); - } - break - ; - case KeyEvent.VK_H: - { - boolean toggleSeqs = !evt.isControlDown(); - boolean toggleCols = !evt.isShiftDown(); + case KeyEvent.VK_ENTER: + case KeyEvent.VK_COMMA: + if (viewport.cursorMode) + { + alignPanel.seqPanel.setCursorRowAndColumn(); + } + break; - boolean hide = false; + case KeyEvent.VK_Q: + if (viewport.cursorMode) + { + alignPanel.seqPanel.setSelectionAreaAtCursor(true); + } + break; + case KeyEvent.VK_M: + if (viewport.cursorMode) + { + alignPanel.seqPanel.setSelectionAreaAtCursor(false); + } + break; - SequenceGroup sg = viewport.getSelectionGroup(); - if (toggleSeqs) - { - if (sg != null && sg.getSize() != viewport.alignment.getHeight()) - { - hideSelSequences_actionPerformed(null); - hide = true; - } - else if (! (toggleCols && - viewport.colSel.getSelected().size() > 0)) - { - showAllSeqs_actionPerformed(null); - } - } + case KeyEvent.VK_F2: + viewport.cursorMode = !viewport.cursorMode; + statusBar.setText("Keyboard editing mode is " + + (viewport.cursorMode ? "on" : "off")); + if (viewport.cursorMode) + { + alignPanel.seqPanel.seqCanvas.cursorX = viewport.startRes; + alignPanel.seqPanel.seqCanvas.cursorY = viewport.startSeq; + } + alignPanel.seqPanel.seqCanvas.repaint(); + break; - if (toggleCols) - { - if (viewport.colSel.getSelected().size() > 0) - { - hideSelColumns_actionPerformed(null); - if (!toggleSeqs) - { - viewport.selectionGroup = sg; - } - } - else if (!hide) - { - showAllColumns_actionPerformed(null); - } - } - break; - } - case KeyEvent.VK_PAGE_UP: - if (viewport.wrapAlignment) - { - alignPanel.scrollUp(true); - } - else - { - alignPanel.setScrollValues(viewport.startRes, - viewport.startSeq - - viewport.endSeq + viewport.startSeq); - } - break; - case KeyEvent.VK_PAGE_DOWN: - if (viewport.wrapAlignment) - { - alignPanel.scrollUp(false); - } - else - { - alignPanel.setScrollValues(viewport.startRes, - viewport.startSeq - + viewport.endSeq - viewport.startSeq); - } - break; + case KeyEvent.VK_F1: + try + { + ClassLoader cl = jalview.gui.Desktop.class.getClassLoader(); + java.net.URL url = javax.help.HelpSet.findHelpSet(cl, + "help/help"); + javax.help.HelpSet hs = new javax.help.HelpSet(cl, url); + + javax.help.HelpBroker hb = hs.createHelpBroker(); + hb.setCurrentID("home"); + hb.setDisplayed(true); + } 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.wrapAlignment) + { + alignPanel.scrollUp(true); + } + else + { + alignPanel.setScrollValues(viewport.startRes, viewport.startSeq + - viewport.endSeq + viewport.startSeq); + } + break; + case KeyEvent.VK_PAGE_DOWN: + if (viewport.wrapAlignment) + { + alignPanel.scrollUp(false); + } + else + { + alignPanel.setScrollValues(viewport.startRes, viewport.startSeq + + viewport.endSeq - viewport.startSeq); } + break; } + } public void keyReleased(KeyEvent evt) { - switch(evt.getKeyCode()) + 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; + 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) + public void addAlignmentPanel(final AlignmentPanel ap, boolean newPanel) { ap.alignFrame = this; @@ -412,9 +562,9 @@ public class AlignFrame int aSize = alignPanels.size(); - tabbedPane.setVisible(aSize>1 || ap.av.viewName!=null); + tabbedPane.setVisible(aSize > 1 || ap.av.viewName != null); - if (aSize == 1 && ap.av.viewName==null) + if (aSize == 1 && ap.av.viewName == null) { this.getContentPane().add(ap, BorderLayout.CENTER); } @@ -432,7 +582,7 @@ public class AlignFrame ap.setVisible(false); } - if(newPanel) + if (newPanel) { if (ap.av.padGaps) { @@ -440,6 +590,7 @@ public class AlignFrame } ap.av.updateConservation(ap); ap.av.updateConsensus(ap); + ap.av.updateStrucConsensus(ap); } } @@ -449,11 +600,10 @@ public class AlignFrame gatherViews.setEnabled(true); tabbedPane.setVisible(true); AlignmentPanel first = (AlignmentPanel) alignPanels.firstElement(); - tabbedPane.addTab(first.av.viewName,first); + tabbedPane.addTab(first.av.viewName, first); this.getContentPane().add(tabbedPane, BorderLayout.CENTER); } - public AlignViewport getViewport() { return viewport; @@ -463,56 +613,81 @@ public class AlignFrame 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(); - } - } - }); + Desktop.instance.addJalviewPropertyChangeListener("services", + thisListener = new java.beans.PropertyChangeListener() + { + public void propertyChange(PropertyChangeEvent evt) + { + // // System.out.println("Discoverer property change."); + // if (evt.getPropertyName().equals("services")) + { + SwingUtilities.invokeLater(new Runnable() + { - addInternalFrameListener(new javax.swing.event. - InternalFrameAdapter() + public void run() + { + System.err + .println("Rebuild WS Menu for service change"); + BuildWebServiceMenu(); + } + + }); + } + } + }); + addInternalFrameListener(new javax.swing.event.InternalFrameAdapter() { public void internalFrameClosed( - javax.swing.event.InternalFrameEvent evt) + javax.swing.event.InternalFrameEvent evt) { - // System.out.println("deregistering discoverer listener"); - Desktop.discoverer.removePropertyChangeListener(thisListener); + 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() + { + public void run() + { + BuildWebServiceMenu(); + } + }).start(); } public void setGUINucleotide(boolean nucleotide) { - showTranslation.setVisible( nucleotide ); - conservationMenuItem.setEnabled( !nucleotide ); - modifyConservation.setEnabled( !nucleotide ); - - //Remember AlignFrame always starts as protein - if(!nucleotide) - { - calculateMenu.remove(calculateMenu.getItemCount()-2); - } - setShowProductsEnabled(); + showTranslation.setVisible(nucleotide); + conservationMenuItem.setEnabled(!nucleotide); + modifyConservation.setEnabled(!nucleotide); + showGroupConservation.setEnabled(!nucleotide); + rnahelicesColour.setEnabled(nucleotide); + purinePyrimidineColour.setEnabled(nucleotide); + // Remember AlignFrame always starts as protein + //if (!nucleotide) + // { + // showTr + // calculateMenu.remove(calculateMenu.getItemCount() - 2); + // } } - + /** + * set up menus for the currently 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. + */ + 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 + * 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) { @@ -522,6 +697,7 @@ public class AlignFrame conservationMenuItem.setSelected(av.getConservationSelected()); seqLimits.setSelected(av.getShowJVSuffix()); idRightAlign.setSelected(av.rightAlignIds); + centreColumnLabelsMenuItem.setState(av.centreColumnLabels); renderGapsMenuItem.setSelected(av.renderGaps); wrapMenuItem.setSelected(av.wrapAlignment); scaleAbove.setVisible(av.wrapAlignment); @@ -530,41 +706,63 @@ public class AlignFrame annotationPanelMenuItem.setState(av.showAnnotation); viewBoxesMenuItem.setSelected(av.showBoxes); viewTextMenuItem.setSelected(av.showText); - - setColourSelected(ColourSchemeProperty. - getColourName(av.getGlobalColourScheme())); + showNonconservedMenuItem.setSelected(av.showUnconserved); + showGroupConsensus.setSelected(av.showGroupConsensus); + showGroupConservation.setSelected(av.showGroupConservation); + showConsensusHistogram.setSelected(av.showConsensusHistogram); + showSequenceLogo.setSelected(av.showSequenceLogo); + setColourSelected(ColourSchemeProperty.getColourName(av + .getGlobalColourScheme())); showSeqFeatures.setSelected(av.showSequenceFeatures); hiddenMarkers.setState(av.showHiddenMarkers); applyToAllGroups.setState(av.colourAppliesToAllGroups); + showNpFeatsMenuitem.setSelected(av.isShowNpFeats()); + showDbRefsMenuitem.setSelected(av.isShowDbRefs()); + autoCalculate.setSelected(av.autoCalculateConsensus); + sortByTree.setSelected(av.sortByTree); + listenToViewSelections.setSelected(av.followSelection); + rnahelicesColour.setEnabled(av.alignment.hasRNAStructure()); + rnahelicesColour.setSelected(av.getGlobalColourScheme() instanceof jalview.schemes.RNAHelicesColour); + setShowProductsEnabled(); updateEditMenuBar(); } + Hashtable progressBars, progressBarHandlers; - Hashtable progressBars; + /* + * (non-Javadoc) + * + * @see jalview.gui.IProgressIndicator#setProgressBar(java.lang.String, long) + */ public void setProgressBar(String message, long id) { - if(progressBars == null) + if (progressBars == null) { progressBars = new Hashtable(); + progressBarHandlers = new Hashtable(); } JPanel progressPanel; + Long lId = new Long(id); GridLayout layout = (GridLayout) statusPanel.getLayout(); - if(progressBars.get( new Long(id) )!=null) - { - progressPanel = (JPanel)progressBars.get( new Long(id) ); - statusPanel.remove(progressPanel); - progressBars.remove( progressPanel ); - progressPanel = null; - if(message!=null) + if (progressBars.get(lId) != null) + { + progressPanel = (JPanel) progressBars.get(new Long(id)); + statusPanel.remove(progressPanel); + progressBars.remove(lId); + progressPanel = null; + if (message != null) { - statusBar.setText(message); + statusBar.setText(message); } - - layout.setRows(layout.getRows() - 1); - } + if (progressBarHandlers.contains(lId)) + { + progressBarHandlers.remove(lId); + } + layout.setRows(layout.getRows() - 1); + } else { progressPanel = new JPanel(new BorderLayout(10, 5)); @@ -578,21 +776,62 @@ public class AlignFrame layout.setRows(layout.getRows() + 1); statusPanel.add(progressPanel); - progressBars.put(new Long(id), progressPanel); + progressBars.put(lId, progressPanel); } - + // update GUI + // setMenusForViewport(); validate(); } + public void registerHandler(final long id, + final IProgressIndicatorHandler handler) + { + if (progressBarHandlers == null || !progressBars.contains(new Long(id))) + { + throw new Error( + "call setProgressBar before registering the progress bar's handler."); + } + progressBarHandlers.put(new Long(id), handler); + final JPanel progressPanel = (JPanel) progressBars.get(new Long(id)); + if (handler.canCancel()) + { + JButton cancel = new JButton("Cancel"); + final IProgressIndicator us = this; + cancel.addActionListener(new ActionListener() + { + public void actionPerformed(ActionEvent e) + { + handler.cancelActivity(id); + us.setProgressBar( + "Cancelled " + + ((JLabel) progressPanel.getComponent(0)) + .getText(), id); + } + }); + progressPanel.add(cancel, BorderLayout.EAST); + } + } + /** + * + * @return true if any progress bars are still active + */ + public boolean operationInProgress() + { + if (progressBars != null && progressBars.size() > 0) + { + return true; + } + return false; + } /* - Added so Castor Mapping file can obtain Jalview Version - */ + * Added so Castor Mapping file can obtain Jalview Version + */ public String getVersion() { - return jalview.bin.Cache.getProperty("VERSION"); + return jalview.bin.Cache.getProperty("VERSION"); } public FeatureRenderer getFeatureRenderer() @@ -600,7 +839,6 @@ public class AlignFrame return alignPanel.seqPanel.seqCanvas.getFeatureRenderer(); } - public void fetchSequence_actionPerformed(ActionEvent e) { new SequenceFetcher(this); @@ -613,31 +851,32 @@ public class AlignFrame public void reload_actionPerformed(ActionEvent e) { - if(fileName!=null) + if (fileName != null) { - if(currentFileFormat.equals("Jalview")) + // 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 -1) + { + currentFileFormat = currentFileFormat.substring(0, + currentFileFormat.indexOf(" ")); + } + saveAlignment(fileName, currentFileFormat); } } @@ -740,41 +993,50 @@ public class AlignFrame if (shortName.indexOf(java.io.File.separatorChar) > -1) { - shortName = shortName.substring(shortName.lastIndexOf( - java.io.File.separatorChar) + 1); + shortName = shortName.substring(shortName + .lastIndexOf(java.io.File.separatorChar) + 1); } success = new Jalview2XML().SaveAlignment(this, file, shortName); - statusBar.setText("Successfully saved to file: " - +fileName+" in " - +format +" format."); + statusBar.setText("Successfully saved to file: " + fileName + " in " + + format + " format."); } else { + if (!jalview.io.AppletFormatAdapter.isValidFormat(format, true)) + { + warningMessage("Cannot save file " + fileName + " using format " + + format, "Alignment output format not supported"); + saveAs_actionPerformed(null); + // JBPNote need to have a raise_gui flag here + return false; + } String[] omitHidden = null; if (viewport.hasHiddenColumns) { - int reply = JOptionPane.showInternalConfirmDialog(Desktop.desktop, - "The Alignment contains hidden columns." - + "\nDo you want to save only the visible alignment?", - "Save / Omit Hidden Columns", - JOptionPane.YES_NO_OPTION, JOptionPane.QUESTION_MESSAGE); + int reply = JOptionPane + .showInternalConfirmDialog( + Desktop.desktop, + "The Alignment contains hidden columns." + + "\nDo you want to save only the visible alignment?", + "Save / Omit Hidden Columns", + JOptionPane.YES_NO_OPTION, + JOptionPane.QUESTION_MESSAGE); if (reply == JOptionPane.YES_OPTION) { omitHidden = viewport.getViewAsString(false); - } + } } FormatAdapter f = new FormatAdapter(); - - String output = f.formatSequences( - format, - (Alignment) viewport.alignment, // class cast exceptions will occur in the distant future - omitHidden, f.getCacheSuffixDefault(format)); + String output = f.formatSequences(format, + (Alignment) viewport.alignment, // class cast exceptions will + // occur in the distant future + omitHidden, f.getCacheSuffixDefault(format), viewport.colSel); if (output == null) { @@ -785,16 +1047,14 @@ public class AlignFrame try { java.io.PrintWriter out = new java.io.PrintWriter( - new java.io.FileWriter(file)); + new java.io.FileWriter(file)); out.print(output); out.close(); this.setTitle(file); - statusBar.setText("Successfully saved to file: " - + fileName + " in " - + format + " format."); - } - catch (Exception ex) + statusBar.setText("Successfully saved to file: " + fileName + + " in " + format + " format."); + } catch (Exception ex) { success = false; ex.printStackTrace(); @@ -804,33 +1064,50 @@ public class AlignFrame if (!success) { - JOptionPane.showInternalMessageDialog( - this, "Couldn't save file: " + fileName, - "Error Saving File", - JOptionPane.WARNING_MESSAGE); + JOptionPane.showInternalMessageDialog(this, "Couldn't save file: " + + fileName, "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! + * + * @param e + * DOCUMENT ME! */ protected void outputText_actionPerformed(ActionEvent e) { - String [] omitHidden = null; + String[] omitHidden = null; - if(viewport.hasHiddenColumns) + if (viewport.hasHiddenColumns) { - int reply = JOptionPane.showInternalConfirmDialog(Desktop.desktop, - "The Alignment contains hidden columns." - +"\nDo you want to output only the visible alignment?", - "Save / Omit Hidden Columns", - JOptionPane.YES_NO_OPTION, JOptionPane.QUESTION_MESSAGE); + int reply = JOptionPane + .showInternalConfirmDialog( + Desktop.desktop, + "The Alignment contains hidden columns." + + "\nDo you want to output only the visible alignment?", + "Save / Omit Hidden Columns", + JOptionPane.YES_NO_OPTION, + JOptionPane.QUESTION_MESSAGE); - if(reply==JOptionPane.YES_OPTION) + if (reply == JOptionPane.YES_OPTION) { omitHidden = viewport.getViewAsString(false); } @@ -838,27 +1115,32 @@ public class AlignFrame CutAndPasteTransfer cap = new CutAndPasteTransfer(); cap.setForInput(null); - Desktop.addInternalFrame(cap, - "Alignment output - " + e.getActionCommand(), 600, - 500); + try + { + cap.setText(new FormatAdapter().formatSequences(e.getActionCommand(), + viewport.alignment, omitHidden, viewport.colSel)); + Desktop.addInternalFrame(cap, + "Alignment output - " + e.getActionCommand(), 600, 500); + } catch (OutOfMemoryError oom) + { + new OOMWarning("Outputting alignment as " + e.getActionCommand(), oom); + cap.dispose(); + } - cap.setText(new FormatAdapter().formatSequences( - e.getActionCommand(), - viewport.alignment, - omitHidden)); } /** * DOCUMENT ME! - * - * @param e DOCUMENT ME! + * + * @param e + * DOCUMENT ME! */ protected void htmlMenuItem_actionPerformed(ActionEvent e) { new HTMLOutput(alignPanel, - alignPanel.seqPanel.seqCanvas.getSequenceRenderer(), - alignPanel.seqPanel.seqCanvas.getFeatureRenderer()); + alignPanel.seqPanel.seqCanvas.getSequenceRenderer(), + alignPanel.seqPanel.seqCanvas.getFeatureRenderer()); } public void createImageMap(File file, String image) @@ -868,8 +1150,9 @@ public class AlignFrame /** * DOCUMENT ME! - * - * @param e DOCUMENT ME! + * + * @param e + * DOCUMENT ME! */ public void createPNG(File f) { @@ -878,15 +1161,15 @@ public class AlignFrame /** * DOCUMENT ME! - * - * @param e DOCUMENT ME! + * + * @param e + * DOCUMENT ME! */ public void createEPS(File f) { alignPanel.makeEPS(f); } - public void pageSetup_actionPerformed(ActionEvent e) { PrinterJob printJob = PrinterJob.getPrinterJob(); @@ -895,12 +1178,13 @@ public class AlignFrame /** * DOCUMENT ME! - * - * @param e DOCUMENT ME! + * + * @param e + * DOCUMENT ME! */ public void printMenuItem_actionPerformed(ActionEvent e) { - //Putting in a thread avoids Swing painting problems + // Putting in a thread avoids Swing painting problems PrintThread thread = new PrintThread(alignPanel); thread.start(); } @@ -910,24 +1194,21 @@ public class AlignFrame new AnnotationExporter().exportFeatures(alignPanel); } - public void exportAnnotations_actionPerformed(ActionEvent e) { new AnnotationExporter().exportAnnotations( - alignPanel, - viewport.showAnnotation ? viewport.alignment.getAlignmentAnnotation() : null, - viewport.alignment.getGroups(), - ((Alignment)viewport.alignment).alignmentProperties - ); + alignPanel, + viewport.showAnnotation ? viewport.alignment + .getAlignmentAnnotation() : null, viewport.alignment + .getGroups(), + ((Alignment) viewport.alignment).alignmentProperties); } - public void associatedData_actionPerformed(ActionEvent e) { // Pick the tree file - JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache. - getProperty( - "LAST_DIRECTORY")); + JalviewFileChooser chooser = new JalviewFileChooser( + jalview.bin.Cache.getProperty("LAST_DIRECTORY")); chooser.setFileView(new JalviewFileView()); chooser.setDialogTitle("Load Jalview Annotations or Features File"); chooser.setToolTipText("Load Jalview Annotations / Features file"); @@ -938,76 +1219,86 @@ public class AlignFrame { String choice = chooser.getSelectedFile().getPath(); jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice); - loadJalviewDataFile(choice); + loadJalviewDataFile(choice, null, null, null); } } - /** - * DOCUMENT ME! - * - * @param e DOCUMENT ME! + * 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 */ public void closeMenuItem_actionPerformed(boolean closeAllTabs) { - if(alignPanels!=null && alignPanels.size()<2) + if (alignPanels != null && alignPanels.size() < 2) { closeAllTabs = true; } try { - if(alignPanels!=null) + if (alignPanels != null) { if (closeAllTabs) { - for (int i = 0; i < alignPanels.size(); i++) + if (this.isClosed()) { - AlignmentPanel ap = (AlignmentPanel) alignPanels.elementAt(i); - jalview.structure.StructureSelectionManager.getStructureSelectionManager() - .removeStructureViewerListener(ap.seqPanel, null); - PaintRefresher.RemoveComponent(ap.seqPanel.seqCanvas); - PaintRefresher.RemoveComponent(ap.idPanel.idCanvas); - PaintRefresher.RemoveComponent(ap); - ap.av.alignment = null; + // really close all the windows - otherwise wait till + // setClosed(true) is called + for (int i = 0; i < alignPanels.size(); i++) + { + AlignmentPanel ap = (AlignmentPanel) alignPanels.elementAt(i); + ap.closePanel(); + } } } else { - int index = tabbedPane.getSelectedIndex(); - - alignPanels.removeElement(alignPanel); - PaintRefresher.RemoveComponent(alignPanel.seqPanel.seqCanvas); - PaintRefresher.RemoveComponent(alignPanel.idPanel.idCanvas); - PaintRefresher.RemoveComponent(alignPanel); - viewport.alignment = null; - alignPanel = null; - viewport = null; - - tabbedPane.removeTabAt(index); - tabbedPane.validate(); - - if(index==tabbedPane.getTabCount()) - { - index --; - } - - this.tabSelectionChanged(index); + closeView(alignPanel); } } if (closeAllTabs) { this.setClosed(true); - } - } - catch (Exception ex) + } + } catch (Exception ex) { ex.printStackTrace(); } } + /** + * close alignPanel2 and shuffle tabs appropriately. + * + * @param alignPanel2 + */ + public void closeView(AlignmentPanel alignPanel2) + { + int index = tabbedPane.getSelectedIndex(); + int closedindex = tabbedPane.indexOfComponent(alignPanel2); + alignPanels.removeElement(alignPanel2); + // Unnecessary + // if (viewport == alignPanel2.av) + // { + // viewport = null; + // } + alignPanel2.closePanel(); + alignPanel2 = 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! @@ -1041,73 +1332,79 @@ public class AlignFrame } } - public void addHistoryItem(CommandI command) { - if(command.getSize()>0) + if (command.getSize() > 0) { viewport.historyList.push(command); viewport.redoList.clear(); updateEditMenuBar(); - viewport.hasHiddenColumns = viewport.colSel.getHiddenColumns() != null; + viewport.hasHiddenColumns = (viewport.colSel != null + && viewport.colSel.getHiddenColumns() != null && viewport.colSel + .getHiddenColumns().size() > 0); } } /** - * + * * @return alignment objects for all views */ AlignmentI[] getViewAlignments() { - if (alignPanels!=null) + if (alignPanels != null) { Enumeration e = alignPanels.elements(); AlignmentI[] als = new AlignmentI[alignPanels.size()]; - for (int i=0; e.hasMoreElements(); i++) + for (int i = 0; e.hasMoreElements(); i++) { als[i] = ((AlignmentPanel) e.nextElement()).av.getAlignment(); } return als; } - if (viewport!=null) + if (viewport != null) { - return new AlignmentI[] { viewport.alignment }; + return new AlignmentI[] + { viewport.alignment }; } return null; } + /** * DOCUMENT ME! - * - * @param e DOCUMENT ME! + * + * @param e + * DOCUMENT ME! */ protected void undoMenuItem_actionPerformed(ActionEvent e) { if (viewport.historyList.empty()) return; - CommandI command = (CommandI)viewport.historyList.pop(); + CommandI command = (CommandI) viewport.historyList.pop(); viewport.redoList.push(command); command.undoCommand(getViewAlignments()); AlignViewport originalSource = getOriginatingSource(command); updateEditMenuBar(); - if(originalSource!=null) + if (originalSource != null) { - originalSource.hasHiddenColumns = viewport.colSel.getHiddenColumns() != null; - originalSource.firePropertyChange("alignment", - null, - originalSource.alignment.getSequences()); + originalSource.hasHiddenColumns = (viewport.colSel != null + && viewport.colSel.getHiddenColumns() != null && viewport.colSel + .getHiddenColumns().size() > 0); + originalSource.firePropertyChange("alignment", null, + originalSource.alignment.getSequences()); } } /** * DOCUMENT ME! - * - * @param e DOCUMENT ME! + * + * @param e + * DOCUMENT ME! */ protected void redoMenuItem_actionPerformed(ActionEvent e) { - if(viewport.redoList.size()<1) + if (viewport.redoList.size() < 1) { return; } @@ -1119,36 +1416,37 @@ public class AlignFrame AlignViewport originalSource = getOriginatingSource(command); updateEditMenuBar(); - if(originalSource!=null) + if (originalSource != null) { - originalSource.hasHiddenColumns = viewport.colSel.getHiddenColumns() != null; - originalSource.firePropertyChange("alignment", - null, - originalSource.alignment.getSequences()); + originalSource.hasHiddenColumns = (viewport.colSel != null + && viewport.colSel.getHiddenColumns() != null && viewport.colSel + .getHiddenColumns().size() > 0); + originalSource.firePropertyChange("alignment", null, + originalSource.alignment.getSequences()); } } AlignViewport getOriginatingSource(CommandI command) { AlignViewport originalSource = null; - //For sequence removal and addition, we need to fire - //the property change event FROM the viewport where the - //original alignment was altered - AlignmentI al=null; + // For sequence removal and addition, we need to fire + // the property change event FROM the viewport where the + // original alignment was altered + AlignmentI al = null; if (command instanceof EditCommand) { EditCommand editCommand = (EditCommand) command; al = editCommand.getAlignment(); - Vector comps = (Vector) PaintRefresher.components - .get(viewport.getSequenceSetId()); + Vector comps = (Vector) PaintRefresher.components.get(viewport + .getSequenceSetId()); for (int i = 0; i < comps.size(); i++) { if (comps.elementAt(i) instanceof AlignmentPanel) { - if (al == ( (AlignmentPanel) comps.elementAt(i)).av.alignment) + if (al == ((AlignmentPanel) comps.elementAt(i)).av.alignment) { - originalSource = ( (AlignmentPanel) comps.elementAt(i)).av; + originalSource = ((AlignmentPanel) comps.elementAt(i)).av; break; } } @@ -1157,8 +1455,8 @@ public class AlignFrame if (originalSource == null) { - //The original view is closed, we must validate - //the current view against the closed view first + // The original view is closed, we must validate + // the current view against the closed view first if (al != null) { PaintRefresher.validateSequences(al, viewport.alignment); @@ -1172,8 +1470,9 @@ public class AlignFrame /** * DOCUMENT ME! - * - * @param up DOCUMENT ME! + * + * @param up + * DOCUMENT ME! */ public void moveSelectedSequences(boolean up) { @@ -1232,25 +1531,23 @@ public class AlignFrame alignPanel.paintAlignment(true); } - - - synchronized void slideSequences(boolean right, int size) { Vector sg = new Vector(); - if(viewport.cursorMode) + if (viewport.cursorMode) + { + sg.addElement(viewport.alignment + .getSequenceAt(alignPanel.seqPanel.seqCanvas.cursorY)); + } + else if (viewport.getSelectionGroup() != null + && viewport.getSelectionGroup().getSize() != viewport.alignment + .getHeight()) { - sg.addElement(viewport.alignment.getSequenceAt( - alignPanel.seqPanel.seqCanvas.cursorY)); + sg = viewport.getSelectionGroup().getSequences( + viewport.hiddenRepSequences); } - else if(viewport.getSelectionGroup()!=null - && viewport.getSelectionGroup().getSize()!=viewport.alignment.getHeight()) - { - sg = viewport.getSelectionGroup().getSequences( - viewport.hiddenRepSequences); - } - if(sg.size()<1) + if (sg.size() < 1) { return; } @@ -1259,8 +1556,8 @@ public class AlignFrame for (int i = 0; i < viewport.alignment.getHeight(); i++) { - if(!sg.contains(viewport.alignment.getSequenceAt(i))) - invertGroup.add(viewport.alignment.getSequenceAt(i)); + if (!sg.contains(viewport.alignment.getSequenceAt(i))) + invertGroup.add(viewport.alignment.getSequenceAt(i)); } SequenceI[] seqs1 = new SequenceI[sg.size()]; @@ -1273,15 +1570,11 @@ public class AlignFrame SlideSequencesCommand ssc; if (right) - ssc = new SlideSequencesCommand("Slide Sequences", - seqs2, seqs1, size, - viewport.getGapCharacter() - ); + ssc = new SlideSequencesCommand("Slide Sequences", seqs2, seqs1, + size, viewport.getGapCharacter()); else - ssc = new SlideSequencesCommand("Slide Sequences", - seqs1, seqs2, size, - viewport.getGapCharacter() - ); + ssc = new SlideSequencesCommand("Slide Sequences", seqs1, seqs2, + size, viewport.getGapCharacter()); int groupAdjustment = 0; if (ssc.getGapsInsertedBegin() && right) @@ -1294,7 +1587,7 @@ public class AlignFrame else if (!ssc.getGapsInsertedBegin() && !right) { if (viewport.cursorMode) - alignPanel.seqPanel.moveCursor( -size, 0); + alignPanel.seqPanel.moveCursor(-size, 0); else groupAdjustment = -size; } @@ -1302,33 +1595,31 @@ public class AlignFrame if (groupAdjustment != 0) { viewport.getSelectionGroup().setStartRes( - viewport.getSelectionGroup().getStartRes() + groupAdjustment); + viewport.getSelectionGroup().getStartRes() + groupAdjustment); viewport.getSelectionGroup().setEndRes( - viewport.getSelectionGroup().getEndRes() + groupAdjustment); + viewport.getSelectionGroup().getEndRes() + groupAdjustment); } - boolean appendHistoryItem = false; - if(viewport.historyList!=null - && viewport.historyList.size()>0 - && viewport.historyList.peek() instanceof SlideSequencesCommand) + if (viewport.historyList != null && viewport.historyList.size() > 0 + && viewport.historyList.peek() instanceof SlideSequencesCommand) { - appendHistoryItem = ssc.appendSlideCommand( - (SlideSequencesCommand)viewport.historyList.peek()) - ; + appendHistoryItem = ssc + .appendSlideCommand((SlideSequencesCommand) viewport.historyList + .peek()); } - if(!appendHistoryItem) + if (!appendHistoryItem) addHistoryItem(ssc); repaint(); } - /** * DOCUMENT ME! - * - * @param e DOCUMENT ME! + * + * @param e + * DOCUMENT ME! */ protected void copy_actionPerformed(ActionEvent e) { @@ -1337,8 +1628,9 @@ public class AlignFrame { return; } - // TODO: preserve the ordering of displayed alignment annotation in any internal paste (particularly sequence associated annotation) - SequenceI [] seqs = viewport.getSelectionAsNewSequence(); + // 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) @@ -1346,72 +1638,56 @@ public class AlignFrame omitHidden = viewport.getViewAsString(true); } - String output = new FormatAdapter().formatSequences( - "Fasta", - seqs, - omitHidden); + String output = new FormatAdapter().formatSequences("Fasta", seqs, + omitHidden); 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!! + // Its really worth setting the clipboard contents + // to empty before setting the large StringSelection!! Toolkit.getDefaultToolkit().getSystemClipboard() - .setContents(new StringSelection(""), null); + .setContents(new StringSelection(""), null); Toolkit.getDefaultToolkit().getSystemClipboard() - .setContents(ss, Desktop.instance); - } - catch (OutOfMemoryError er) + .setContents(ss, Desktop.instance); + } catch (OutOfMemoryError er) { - er.printStackTrace(); - javax.swing.SwingUtilities.invokeLater(new Runnable() - { - public void run() - { - javax.swing.JOptionPane.showInternalMessageDialog(Desktop.desktop, - "Out of memory copying region!!" - + - "\nSee help files for increasing Java Virtual Machine memory." - , "Out of memory", - javax.swing.JOptionPane.WARNING_MESSAGE); - } - }); - + new OOMWarning("copying region", er); return; } Vector hiddenColumns = null; - if(viewport.hasHiddenColumns) + if (viewport.hasHiddenColumns) { - hiddenColumns =new Vector(); - int hiddenOffset = viewport.getSelectionGroup().getStartRes(); - for (int i = 0; i < viewport.getColumnSelection().getHiddenColumns().size(); - i++) + hiddenColumns = new Vector(); + int hiddenOffset = viewport.getSelectionGroup().getStartRes(), hiddenCutoff = viewport + .getSelectionGroup().getEndRes(); + for (int i = 0; i < viewport.getColumnSelection().getHiddenColumns() + .size(); i++) { - int[] region = (int[]) - viewport.getColumnSelection().getHiddenColumns().elementAt(i); - - hiddenColumns.addElement(new int[] - {region[0] - hiddenOffset, - region[1]-hiddenOffset}); + int[] region = (int[]) viewport.getColumnSelection() + .getHiddenColumns().elementAt(i); + if (region[0] >= hiddenOffset && region[1] <= hiddenCutoff) + { + hiddenColumns.addElement(new int[] + { region[0] - hiddenOffset, region[1] - hiddenOffset }); + } } } Desktop.jalviewClipboard = new Object[] - { - seqs, - viewport.alignment.getDataset(), - hiddenColumns}; - statusBar.setText("Copied "+seqs.length+" sequences to clipboard."); + { seqs, viewport.alignment.getDataset(), hiddenColumns }; + statusBar.setText("Copied " + seqs.length + " sequences to clipboard."); } /** * DOCUMENT ME! - * - * @param e DOCUMENT ME! + * + * @param e + * DOCUMENT ME! */ protected void pasteNew_actionPerformed(ActionEvent e) { @@ -1420,8 +1696,9 @@ public class AlignFrame /** * DOCUMENT ME! - * - * @param e DOCUMENT ME! + * + * @param e + * DOCUMENT ME! */ protected void pasteThis_actionPerformed(ActionEvent e) { @@ -1429,13 +1706,14 @@ public class AlignFrame } /** - * DOCUMENT ME! - * - * @param newAlignment DOCUMENT ME! + * 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; + boolean externalPaste = true; try { Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard(); @@ -1457,23 +1735,9 @@ public class AlignFrame format = new IdentifyFile().Identify(str, "Paste"); - } - catch (OutOfMemoryError er) + } catch (OutOfMemoryError er) { - er.printStackTrace(); - javax.swing.SwingUtilities.invokeLater(new Runnable() - { - public void run() - { - javax.swing.JOptionPane.showInternalMessageDialog(Desktop.desktop, - "Out of memory pasting sequences!!" - + - "\nSee help files for increasing Java Virtual Machine memory." - , "Out of memory", - javax.swing.JOptionPane.WARNING_MESSAGE); - } - }); - + new OOMWarning("Out of memory pasting sequences!!", er); return; } @@ -1481,56 +1745,58 @@ public class AlignFrame 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>>This is a fix for the moment, until a better solution is found!!<<< - af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().transferSettings( - alignPanel.seqPanel.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) + } + if (!newAlignment) + { + // ///// + // ADD HISTORY ITEM + // + addHistoryItem(new EditCommand("Add sequences", EditCommand.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) + { + for (int a = 0; a < sequences[i].getAnnotation().length; a++) + { + annotationAdded = true; + sequences[i].getAnnotation()[a].adjustForAlignment(); + sequences[i].getAnnotation()[a].padAnnotation(alwidth); + 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 + alview[avnum].setAnnotationIndex(newann, a); + } + } + } + } + buildSortByAnnotationScoresMenu(); + } + viewport.firePropertyChange("alignment", null, + alignment.getSequences()); + + } + else + { + AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH, + DEFAULT_HEIGHT); + String newtitle = new String("Copied sequences"); + + if (Desktop.jalviewClipboard != null + && Desktop.jalviewClipboard[2] != null) + { + Vector hc = (Vector) Desktop.jalviewClipboard[2]; + for (int i = 0; i < hc.size(); i++) + { + int[] region = (int[]) hc.elementAt(i); + af.viewport.hideColumns(region[0], region[1]); + } + } + + // >>>This is a fix for the moment, until a better solution is + // found!!<<< + af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer() + .transferSettings( + alignPanel.seqPanel.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 + System.out.println("Exception whilst pasting: " + ex); + // could be anything being pasted in here } - } /** * DOCUMENT ME! - * - * @param e DOCUMENT ME! + * + * @param e + * DOCUMENT ME! */ protected void cut_actionPerformed(ActionEvent e) { @@ -1709,8 +1988,9 @@ public class AlignFrame /** * DOCUMENT ME! - * - * @param e DOCUMENT ME! + * + * @param e + * DOCUMENT ME! */ protected void delete_actionPerformed(ActionEvent evt) { @@ -1729,46 +2009,38 @@ public class AlignFrame seqs.addElement(seq); } - - // If the cut affects all sequences, remove highlighted columns - if (sg.getSize() == viewport.alignment.getHeight()) - { - viewport.getColumnSelection().removeElements(sg.getStartRes(), - sg.getEndRes() + 1); - } - - - SequenceI [] cut = new SequenceI[seqs.size()]; - for(int i=0; i 0) { - if(trimLeft) + if (trimLeft) { column = colSel.getMin(); } @@ -1900,43 +2179,35 @@ public class AlignFrame column = colSel.getMax(); } - SequenceI [] seqs; - if(viewport.getSelectionGroup()!=null) + SequenceI[] seqs; + if (viewport.getSelectionGroup() != null) { - seqs = viewport.getSelectionGroup().getSequencesAsArray(viewport. - hiddenRepSequences); + seqs = viewport.getSelectionGroup().getSequencesAsArray( + viewport.hiddenRepSequences); } else { seqs = viewport.alignment.getSequencesArray(); } - TrimRegionCommand trimRegion; - if(trimLeft) + if (trimLeft) { trimRegion = new TrimRegionCommand("Remove Left", - TrimRegionCommand.TRIM_LEFT, - seqs, - column, - viewport.alignment, - viewport.colSel, - viewport.selectionGroup); + TrimRegionCommand.TRIM_LEFT, seqs, column, + viewport.alignment, viewport.colSel, + viewport.selectionGroup); viewport.setStartRes(0); } - else - { - trimRegion = new TrimRegionCommand("Remove Right", - TrimRegionCommand.TRIM_RIGHT, - seqs, - column, - viewport.alignment, - viewport.colSel, - viewport.selectionGroup); - } - - statusBar.setText("Removed "+trimRegion.getSize()+" columns."); + else + { + trimRegion = new TrimRegionCommand("Remove Right", + TrimRegionCommand.TRIM_RIGHT, seqs, column, + viewport.alignment, viewport.colSel, + viewport.selectionGroup); + } + statusBar.setText("Removed " + trimRegion.getSize() + " columns."); addHistoryItem(trimRegion); @@ -1946,32 +2217,33 @@ public class AlignFrame { SequenceGroup sg = (SequenceGroup) groups.get(i); - if ( (trimLeft && !sg.adjustForRemoveLeft(column)) - || (!trimLeft && !sg.adjustForRemoveRight(column))) + if ((trimLeft && !sg.adjustForRemoveLeft(column)) + || (!trimLeft && !sg.adjustForRemoveRight(column))) { viewport.alignment.deleteGroup(sg); } } - viewport.firePropertyChange("alignment", null, - viewport.getAlignment().getSequences()); + viewport.firePropertyChange("alignment", null, viewport + .getAlignment().getSequences()); } } /** * DOCUMENT ME! - * - * @param e DOCUMENT ME! + * + * @param e + * DOCUMENT ME! */ public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e) { - int start = 0, end = viewport.alignment.getWidth()-1; + int start = 0, end = viewport.alignment.getWidth() - 1; SequenceI[] seqs; if (viewport.getSelectionGroup() != null) { - seqs = viewport.getSelectionGroup().getSequencesAsArray(viewport. - hiddenRepSequences); + seqs = viewport.getSelectionGroup().getSequencesAsArray( + viewport.hiddenRepSequences); start = viewport.getSelectionGroup().getStartRes(); end = viewport.getSelectionGroup().getEndRes(); } @@ -1980,46 +2252,44 @@ public class AlignFrame seqs = viewport.alignment.getSequencesArray(); } - - RemoveGapColCommand removeGapCols = - new RemoveGapColCommand("Remove Gapped Columns", - seqs, - start, end, - viewport.alignment); + RemoveGapColCommand removeGapCols = new RemoveGapColCommand( + "Remove Gapped Columns", seqs, start, end, viewport.alignment); addHistoryItem(removeGapCols); - statusBar.setText("Removed "+removeGapCols.getSize()+" empty columns."); + statusBar.setText("Removed " + removeGapCols.getSize() + + " empty columns."); - //This is to maintain viewport position on first residue - //of first sequence + // This is to maintain viewport position on first residue + // of first sequence SequenceI seq = viewport.alignment.getSequenceAt(0); int startRes = seq.findPosition(viewport.startRes); - // ShiftList shifts; - // viewport.getAlignment().removeGaps(shifts=new ShiftList()); - // edit.alColumnChanges=shifts.getInverse(); - // if (viewport.hasHiddenColumns) - // viewport.getColumnSelection().compensateForEdits(shifts); - viewport.setStartRes(seq.findIndex(startRes)-1); - viewport.firePropertyChange("alignment", null, - viewport.getAlignment().getSequences()); + // 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! + * + * @param e + * DOCUMENT ME! */ public void removeAllGapsMenuItem_actionPerformed(ActionEvent e) { - int start = 0, end = viewport.alignment.getWidth()-1; + int start = 0, end = viewport.alignment.getWidth() - 1; SequenceI[] seqs; if (viewport.getSelectionGroup() != null) { - seqs = viewport.getSelectionGroup().getSequencesAsArray(viewport. - hiddenRepSequences); + seqs = viewport.getSelectionGroup().getSequencesAsArray( + viewport.hiddenRepSequences); start = viewport.getSelectionGroup().getStartRes(); end = viewport.getSelectionGroup().getEndRes(); } @@ -2028,41 +2298,49 @@ public class AlignFrame seqs = viewport.alignment.getSequencesArray(); } - //This is to maintain viewport position on first residue - //of first sequence + // This is to maintain viewport position on first residue + // of first sequence SequenceI seq = viewport.alignment.getSequenceAt(0); int startRes = seq.findPosition(viewport.startRes); - addHistoryItem(new RemoveGapsCommand("Remove Gaps", - seqs, - start, end, - viewport.alignment)); + addHistoryItem(new RemoveGapsCommand("Remove Gaps", seqs, start, end, + viewport.alignment)); - viewport.setStartRes(seq.findIndex(startRes)-1); + viewport.setStartRes(seq.findIndex(startRes) - 1); - viewport.firePropertyChange("alignment", null, - viewport.getAlignment().getSequences()); + viewport.firePropertyChange("alignment", null, viewport.getAlignment() + .getSequences()); } /** * DOCUMENT ME! - * - * @param e DOCUMENT ME! + * + * @param e + * DOCUMENT ME! */ public void padGapsMenuitem_actionPerformed(ActionEvent e) { viewport.padGaps = padGapsMenuitem.isSelected(); + viewport.firePropertyChange("alignment", null, viewport.getAlignment() + .getSequences()); + } - viewport.firePropertyChange("alignment", - null, - viewport.getAlignment().getSequences()); + // else + { + // if (justifySeqs>0) + { + // alignment.justify(justifySeqs!=RIGHT_JUSTIFY); + } } + // } + /** * DOCUMENT ME! - * - * @param e DOCUMENT ME! + * + * @param e + * DOCUMENT ME! */ public void findMenuItem_actionPerformed(ActionEvent e) { @@ -2071,8 +2349,57 @@ public class AlignFrame public void newView_actionPerformed(ActionEvent e) { - AlignmentPanel newap = - new Jalview2XML().copyAlignPanel(alignPanel, true); + newView(true); + } + + /** + * + * @param copyAnnotation + * if true then duplicate all annnotation, groups and settings + * @return new alignment panel, already displayed. + */ + public AlignmentPanel newView(boolean copyAnnotation) + { + return newView(null, copyAnnotation); + } + + /** + * + * @param viewTitle + * title of newly created view + * @return new alignment panel, already displayed. + */ + public AlignmentPanel newView(String viewTitle) + { + return newView(viewTitle, true); + } + + /** + * + * @param viewTitle + * title of newly created view + * @param copyAnnotation + * if true then duplicate all annnotation, groups and settings + * @return new alignment panel, already displayed. + */ + public AlignmentPanel newView(String viewTitle, boolean copyAnnotation) + { + AlignmentPanel newap = new Jalview2XML().copyAlignPanel(alignPanel, + true); + if (!copyAnnotation) + { + // just remove all the current annotation except for the automatic stuff + newap.av.alignment.deleteAllGroups(); + for (AlignmentAnnotation alan : newap.av.alignment + .getAlignmentAnnotation()) + { + if (!alan.autoCalculated) + { + newap.av.alignment.deleteAnnotation(alan); + } + ; + } + } newap.av.gatherViewsHere = false; @@ -2085,42 +2412,54 @@ public class AlignFrame newap.av.redoList = viewport.redoList; int index = Desktop.getViewCount(viewport.getSequenceSetId()); - String newViewName = "View " +index; - - Vector comps = (Vector) PaintRefresher.components.get(viewport. - getSequenceSetId()); + // make sure the new view has a unique name - this is essential for Jalview + // 2 archives + boolean addFirstIndex = false; + if (viewTitle == null || viewTitle.trim().length() == 0) + { + viewTitle = "View"; + addFirstIndex = true; + } + else + { + index = 1;// we count from 1 if given a specific name + } + String newViewName = viewTitle + ((addFirstIndex) ? " " + index : ""); + Vector comps = (Vector) PaintRefresher.components.get(viewport + .getSequenceSetId()); Vector existingNames = new Vector(); - for(int i=0; i 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.alignment.getHeight()) + { + hideSelSequences_actionPerformed(null); + hide = true; + } + else if (!(toggleCols && viewport.colSel.getSelected().size() > 0)) + { + showAllSeqs_actionPerformed(null); + } + } + + if (toggleCols) + { + if (viewport.colSel.getSelected().size() > 0) + { + hideSelColumns_actionPerformed(null); + if (!toggleSeqs) + { + viewport.selectionGroup = sg; + } + } + else if (!hide) + { + showAllColumns_actionPerformed(null); + } + } + } + + /* + * (non-Javadoc) + * + * @see + * jalview.jbgui.GAlignFrame#hideAllButSelection_actionPerformed(java.awt. + * event.ActionEvent) + */ + public void hideAllButSelection_actionPerformed(ActionEvent e) + { + toggleHiddenRegions(false, false); + } + + /* + * (non-Javadoc) + * + * @see + * jalview.jbgui.GAlignFrame#hideAllSelection_actionPerformed(java.awt.event + * .ActionEvent) + */ + public void hideAllSelection_actionPerformed(ActionEvent e) + { + SequenceGroup sg = viewport.getSelectionGroup(); + viewport.expandColSelection(sg, false); + viewport.hideAllSelectedSeqs(); + viewport.hideSelectedColumns(); + alignPanel.paintAlignment(true); + } + + /* + * (non-Javadoc) + * + * @see + * jalview.jbgui.GAlignFrame#showAllhidden_actionPerformed(java.awt.event. + * ActionEvent) + */ + public void showAllhidden_actionPerformed(ActionEvent e) + { + viewport.showAllHiddenColumns(); + viewport.showAllHiddenSeqs(); + alignPanel.paintAlignment(true); + } + public void hideSelColumns_actionPerformed(ActionEvent e) { viewport.hideSelectedColumns(); @@ -2218,8 +2687,9 @@ public class AlignFrame /** * DOCUMENT ME! - * - * @param e DOCUMENT ME! + * + * @param e + * DOCUMENT ME! */ protected void scaleAbove_actionPerformed(ActionEvent e) { @@ -2229,8 +2699,9 @@ public class AlignFrame /** * DOCUMENT ME! - * - * @param e DOCUMENT ME! + * + * @param e + * DOCUMENT ME! */ protected void scaleLeft_actionPerformed(ActionEvent e) { @@ -2240,8 +2711,9 @@ public class AlignFrame /** * DOCUMENT ME! - * - * @param e DOCUMENT ME! + * + * @param e + * DOCUMENT ME! */ protected void scaleRight_actionPerformed(ActionEvent e) { @@ -2251,8 +2723,9 @@ public class AlignFrame /** * DOCUMENT ME! - * - * @param e DOCUMENT ME! + * + * @param e + * DOCUMENT ME! */ public void viewBoxesMenuItem_actionPerformed(ActionEvent e) { @@ -2262,8 +2735,9 @@ public class AlignFrame /** * DOCUMENT ME! - * - * @param e DOCUMENT ME! + * + * @param e + * DOCUMENT ME! */ public void viewTextMenuItem_actionPerformed(ActionEvent e) { @@ -2273,8 +2747,9 @@ public class AlignFrame /** * DOCUMENT ME! - * - * @param e DOCUMENT ME! + * + * @param e + * DOCUMENT ME! */ protected void renderGapsMenuItem_actionPerformed(ActionEvent e) { @@ -2282,22 +2757,29 @@ public class AlignFrame alignPanel.paintAlignment(true); } - public FeatureSettings featureSettings; + public void featureSettings_actionPerformed(ActionEvent e) { - if(featureSettings !=null ) + 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); } /** - * DOCUMENT ME! - * - * @param evt DOCUMENT ME! + * Set or clear 'Show Sequence Features' + * + * @param evt + * DOCUMENT ME! */ public void showSeqFeatures_actionPerformed(ActionEvent evt) { @@ -2310,9 +2792,33 @@ public class AlignFrame } /** + * Set or clear 'Show Sequence Features' + * + * @param evt + * DOCUMENT ME! + */ + public void showSeqFeaturesHeight_actionPerformed(ActionEvent evt) + { + viewport.setShowSequenceFeaturesHeight(showSeqFeaturesHeight + .isSelected()); + if (viewport.getShowSequenceFeaturesHeight()) + { + // ensure we're actually displaying features + viewport.setShowSequenceFeatures(true); + showSeqFeatures.setSelected(true); + } + alignPanel.paintAlignment(true); + if (alignPanel.getOverviewPanel() != null) + { + alignPanel.getOverviewPanel().updateOverviewImage(); + } + } + + /** * DOCUMENT ME! - * - * @param e DOCUMENT ME! + * + * @param e + * DOCUMENT ME! */ public void annotationPanelMenuItem_actionPerformed(ActionEvent e) { @@ -2322,67 +2828,23 @@ public class AlignFrame public void alignmentProperties() { - JEditorPane editPane = new JEditorPane("text/html",""); + JEditorPane editPane = new JEditorPane("text/html", ""); editPane.setEditable(false); - StringBuffer contents = new StringBuffer(""); - - float avg = 0; - int min=Integer.MAX_VALUE, max=0; - for(int i=0; imax) - max = size; - if(sizeSequences: "+ viewport.alignment.getHeight()); - contents.append("
Minimum Sequence Length: "+min); - contents.append("
Maximum Sequence Length: "+max); - contents.append("
Average Length: "+(int)avg); - - if (((Alignment)viewport.alignment).getProperties() != null) - { - Hashtable props = ((Alignment)viewport.alignment).getProperties(); - Enumeration en = props.keys(); - contents.append("

"); - while(en.hasMoreElements()) - { - String key = en.nextElement().toString(); - StringBuffer val = new StringBuffer(); - String vals = props.get(key).toString(); - int pos=0, npos; - do { - npos = vals.indexOf("\n",pos); - if (npos==-1) - { - val.append(vals.substring(pos)); - } else { - val.append(vals.substring(pos, npos)); - val.append("
"); - } - pos = npos+1; - } while (npos!=-1); - contents.append(""); - } - contents.append("
"+key+""+val+"
"); - } - editPane.setText(contents.toString()+""); + StringBuffer contents = new AlignmentProperties(viewport.alignment) + .formatAsHtml(); + editPane.setText("" + contents.toString() + ""); JInternalFrame frame = new JInternalFrame(); frame.getContentPane().add(new JScrollPane(editPane)); - Desktop.instance.addInternalFrame(frame,"Alignment Properties: "+getTitle(),500,400); + Desktop.instance.addInternalFrame(frame, "Alignment Properties: " + + getTitle(), 500, 400); } - /** * DOCUMENT ME! - * - * @param e DOCUMENT ME! + * + * @param e + * DOCUMENT ME! */ public void overviewMenuItem_actionPerformed(ActionEvent e) { @@ -2395,17 +2857,16 @@ public class AlignFrame OverviewPanel overview = new OverviewPanel(alignPanel); frame.setContentPane(overview); Desktop.addInternalFrame(frame, "Overview " + this.getTitle(), - frame.getWidth(), frame.getHeight()); + frame.getWidth(), frame.getHeight()); frame.pack(); frame.setLayer(JLayeredPane.PALETTE_LAYER); frame.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter() { public void internalFrameClosed( - javax.swing.event.InternalFrameEvent evt) + javax.swing.event.InternalFrameEvent evt) { alignPanel.setOverviewPanel(null); - } - ; + }; }); alignPanel.setOverviewPanel(overview); @@ -2418,8 +2879,9 @@ public class AlignFrame /** * DOCUMENT ME! - * - * @param e DOCUMENT ME! + * + * @param e + * DOCUMENT ME! */ protected void noColourmenuItem_actionPerformed(ActionEvent e) { @@ -2428,19 +2890,22 @@ public class AlignFrame /** * DOCUMENT ME! - * - * @param e DOCUMENT ME! + * + * @param e + * DOCUMENT ME! */ public void clustalColour_actionPerformed(ActionEvent e) { changeColour(new ClustalxColourScheme( - viewport.alignment.getSequences(), viewport.alignment.getWidth())); + viewport.alignment.getSequences(), + viewport.alignment.getWidth())); } /** * DOCUMENT ME! - * - * @param e DOCUMENT ME! + * + * @param e + * DOCUMENT ME! */ public void zappoColour_actionPerformed(ActionEvent e) { @@ -2449,8 +2914,9 @@ public class AlignFrame /** * DOCUMENT ME! - * - * @param e DOCUMENT ME! + * + * @param e + * DOCUMENT ME! */ public void taylorColour_actionPerformed(ActionEvent e) { @@ -2459,8 +2925,9 @@ public class AlignFrame /** * DOCUMENT ME! - * - * @param e DOCUMENT ME! + * + * @param e + * DOCUMENT ME! */ public void hydrophobicityColour_actionPerformed(ActionEvent e) { @@ -2469,8 +2936,9 @@ public class AlignFrame /** * DOCUMENT ME! - * - * @param e DOCUMENT ME! + * + * @param e + * DOCUMENT ME! */ public void helixColour_actionPerformed(ActionEvent e) { @@ -2479,8 +2947,9 @@ public class AlignFrame /** * DOCUMENT ME! - * - * @param e DOCUMENT ME! + * + * @param e + * DOCUMENT ME! */ public void strandColour_actionPerformed(ActionEvent e) { @@ -2489,8 +2958,9 @@ public class AlignFrame /** * DOCUMENT ME! - * - * @param e DOCUMENT ME! + * + * @param e + * DOCUMENT ME! */ public void turnColour_actionPerformed(ActionEvent e) { @@ -2499,8 +2969,9 @@ public class AlignFrame /** * DOCUMENT ME! - * - * @param e DOCUMENT ME! + * + * @param e + * DOCUMENT ME! */ public void buriedColour_actionPerformed(ActionEvent e) { @@ -2509,24 +2980,40 @@ public class AlignFrame /** * DOCUMENT ME! - * - * @param e DOCUMENT ME! + * + * @param e + * DOCUMENT ME! */ public void nucleotideColour_actionPerformed(ActionEvent e) { changeColour(new NucleotideColourScheme()); } + public void purinePyrimidineColour_actionPerformed(ActionEvent e) + { + changeColour(new PurinePyrimidineColourScheme()); + } + /* + public void covariationColour_actionPerformed(ActionEvent e) + { + changeColour(new CovariationColourScheme(viewport.alignment.getAlignmentAnnotation()[0])); + } + */ public void annotationColour_actionPerformed(ActionEvent e) { new AnnotationColourChooser(viewport, alignPanel); } - + + public void rnahelicesColour_actionPerformed(ActionEvent e) + { + new RNAHelicesColourChooser(viewport, alignPanel); + } /** * DOCUMENT ME! - * - * @param e DOCUMENT ME! + * + * @param e + * DOCUMENT ME! */ protected void applyToAllGroups_actionPerformed(ActionEvent e) { @@ -2535,22 +3022,22 @@ public class AlignFrame /** * DOCUMENT ME! - * - * @param cs DOCUMENT ME! + * + * @param cs + * DOCUMENT ME! */ public void changeColour(ColourSchemeI cs) { int threshold = 0; - if(cs!=null) + if (cs != null) { if (viewport.getAbovePIDThreshold()) { threshold = SliderPanel.setPIDSliderSource(alignPanel, cs, - "Background"); + "Background"); - cs.setThreshold(threshold, - viewport.getIgnoreGapsConsensus()); + cs.setThreshold(threshold, viewport.getIgnoreGapsConsensus()); viewport.setGlobalColourScheme(cs); } @@ -2564,17 +3051,16 @@ public class AlignFrame Alignment al = (Alignment) viewport.alignment; Conservation c = new Conservation("All", - ResidueProperties.propHash, 3, - al.getSequences(), 0, - al.getWidth() - 1); + ResidueProperties.propHash, 3, al.getSequences(), 0, + al.getWidth() - 1); c.calculate(); c.verdict(false, viewport.ConsPercGaps); cs.setConservation(c); - cs.setConservationInc(SliderPanel.setConservationSlider(alignPanel, cs, - "Background")); + cs.setConservationInc(SliderPanel.setConservationSlider(alignPanel, + cs, "Background")); } else { @@ -2603,48 +3089,44 @@ public class AlignFrame if (cs instanceof ClustalxColourScheme) { sg.cs = new ClustalxColourScheme( - sg.getSequences(viewport.hiddenRepSequences), sg.getWidth()); + sg.getSequences(viewport.hiddenRepSequences), + sg.getWidth()); } else if (cs instanceof UserColourScheme) { - sg.cs = new UserColourScheme( ( (UserColourScheme) cs).getColours()); + sg.cs = new UserColourScheme(((UserColourScheme) cs).getColours()); } else { try { sg.cs = (ColourSchemeI) cs.getClass().newInstance(); - } - catch (Exception ex) + } catch (Exception ex) { } } if (viewport.getAbovePIDThreshold() - || cs instanceof PIDColourScheme - || cs instanceof Blosum62ColourScheme) + || cs instanceof PIDColourScheme + || cs instanceof Blosum62ColourScheme) { - sg.cs.setThreshold(threshold, - viewport.getIgnoreGapsConsensus()); + sg.cs.setThreshold(threshold, viewport.getIgnoreGapsConsensus()); - sg.cs.setConsensus(AAFrequency.calculate( - sg.getSequences(viewport.hiddenRepSequences), sg.getStartRes(), - sg.getEndRes()+1)); - } + sg.cs.setConsensus(AAFrequency.calculate( + sg.getSequences(viewport.hiddenRepSequences), + sg.getStartRes(), sg.getEndRes() + 1)); + } else { sg.cs.setThreshold(0, viewport.getIgnoreGapsConsensus()); } - if (viewport.getConservationSelected()) { Conservation c = new Conservation("Group", - ResidueProperties.propHash, 3, - sg.getSequences(viewport. - hiddenRepSequences), - sg.getStartRes(), - sg.getEndRes()+1); + ResidueProperties.propHash, 3, + sg.getSequences(viewport.hiddenRepSequences), + sg.getStartRes(), sg.getEndRes() + 1); c.calculate(); c.verdict(false, viewport.ConsPercGaps); sg.cs.setConservation(c); @@ -2652,57 +3134,57 @@ public class AlignFrame else { sg.cs.setConservation(null); + } } } - } if (alignPanel.getOverviewPanel() != null) { alignPanel.getOverviewPanel().updateOverviewImage(); } - - - alignPanel.paintAlignment(true); } /** * DOCUMENT ME! - * - * @param e DOCUMENT ME! + * + * @param e + * DOCUMENT ME! */ protected void modifyPID_actionPerformed(ActionEvent e) { - if (viewport.getAbovePIDThreshold() && viewport.globalColourScheme!=null) + if (viewport.getAbovePIDThreshold() + && viewport.globalColourScheme != null) { SliderPanel.setPIDSliderSource(alignPanel, - viewport.getGlobalColourScheme(), - "Background"); + viewport.getGlobalColourScheme(), "Background"); SliderPanel.showPIDSlider(); } } /** * DOCUMENT ME! - * - * @param e DOCUMENT ME! + * + * @param e + * DOCUMENT ME! */ protected void modifyConservation_actionPerformed(ActionEvent e) { - if (viewport.getConservationSelected() && viewport.globalColourScheme!=null) + if (viewport.getConservationSelected() + && viewport.globalColourScheme != null) { SliderPanel.setConservationSlider(alignPanel, - viewport.globalColourScheme, - "Background"); + viewport.globalColourScheme, "Background"); SliderPanel.showConservationSlider(); } } /** * DOCUMENT ME! - * - * @param e DOCUMENT ME! + * + * @param e + * DOCUMENT ME! */ protected void conservationMenuItem_actionPerformed(ActionEvent e) { @@ -2718,8 +3200,9 @@ public class AlignFrame /** * DOCUMENT ME! - * - * @param e DOCUMENT ME! + * + * @param e + * DOCUMENT ME! */ public void abovePIDThreshold_actionPerformed(ActionEvent e) { @@ -2735,8 +3218,9 @@ public class AlignFrame /** * DOCUMENT ME! - * - * @param e DOCUMENT ME! + * + * @param e + * DOCUMENT ME! */ public void userDefinedColour_actionPerformed(ActionEvent e) { @@ -2746,8 +3230,8 @@ public class AlignFrame } else { - UserColourScheme udc = (UserColourScheme) UserDefinedColours. - getUserColourSchemes().get(e.getActionCommand()); + UserColourScheme udc = (UserColourScheme) UserDefinedColours + .getUserColourSchemes().get(e.getActionCommand()); changeColour(udc); } @@ -2760,8 +3244,8 @@ public class AlignFrame int i, iSize = menuItems.length; for (i = 0; i < iSize; i++) { - if (menuItems[i].getName() != null && - menuItems[i].getName().equals("USER_DEFINED")) + if (menuItems[i].getName() != null + && menuItems[i].getName().equals("USER_DEFINED")) { colourMenu.remove(menuItems[i]); iSize--; @@ -2769,47 +3253,47 @@ public class AlignFrame } if (jalview.gui.UserDefinedColours.getUserColourSchemes() != null) { - java.util.Enumeration userColours = jalview.gui.UserDefinedColours. - getUserColourSchemes().keys(); + java.util.Enumeration userColours = jalview.gui.UserDefinedColours + .getUserColourSchemes().keys(); while (userColours.hasMoreElements()) { final JRadioButtonMenuItem radioItem = new JRadioButtonMenuItem( - userColours. - nextElement().toString()); + userColours.nextElement().toString()); radioItem.setName("USER_DEFINED"); radioItem.addMouseListener(new MouseAdapter() + { + public void mousePressed(MouseEvent evt) + { + if (evt.isControlDown() + || SwingUtilities.isRightMouseButton(evt)) { - public void mousePressed(MouseEvent evt) - { - if(evt.isControlDown() || SwingUtilities.isRightMouseButton(evt)) - { - radioItem.removeActionListener(radioItem.getActionListeners()[0]); + radioItem.removeActionListener(radioItem.getActionListeners()[0]); - int option = JOptionPane.showInternalConfirmDialog(jalview.gui. - Desktop.desktop, + int option = JOptionPane.showInternalConfirmDialog( + jalview.gui.Desktop.desktop, "Remove from default list?", "Remove user defined colour", JOptionPane.YES_NO_OPTION); - if(option == JOptionPane.YES_OPTION) + if (option == JOptionPane.YES_OPTION) + { + jalview.gui.UserDefinedColours + .removeColourFromDefaults(radioItem.getText()); + colourMenu.remove(radioItem); + } + else + { + radioItem.addActionListener(new ActionListener() + { + public void actionPerformed(ActionEvent evt) { - jalview.gui.UserDefinedColours.removeColourFromDefaults( - radioItem.getText()); - colourMenu.remove(radioItem); + userDefinedColour_actionPerformed(evt); } - else - { - radioItem.addActionListener(new ActionListener() - { - public void actionPerformed(ActionEvent evt) - { - userDefinedColour_actionPerformed(evt); - } - }); - } + }); } + } } - }); + }); radioItem.addActionListener(new ActionListener() { public void actionPerformed(ActionEvent evt) @@ -2826,8 +3310,9 @@ public class AlignFrame /** * DOCUMENT ME! - * - * @param e DOCUMENT ME! + * + * @param e + * DOCUMENT ME! */ public void PIDColour_actionPerformed(ActionEvent e) { @@ -2836,8 +3321,9 @@ public class AlignFrame /** * DOCUMENT ME! - * - * @param e DOCUMENT ME! + * + * @param e + * DOCUMENT ME! */ public void BLOSUM62Colour_actionPerformed(ActionEvent e) { @@ -2846,27 +3332,29 @@ public class AlignFrame /** * DOCUMENT ME! - * - * @param e DOCUMENT ME! + * + * @param e + * DOCUMENT ME! */ public void sortPairwiseMenuItem_actionPerformed(ActionEvent e) { - SequenceI [] oldOrder = viewport.getAlignment().getSequencesArray(); - AlignmentSorter.sortByPID(viewport.getAlignment(), - viewport.getAlignment().getSequenceAt(0)); + SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray(); + AlignmentSorter.sortByPID(viewport.getAlignment(), viewport + .getAlignment().getSequenceAt(0), null); addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder, - viewport.alignment)); + viewport.alignment)); alignPanel.paintAlignment(true); } /** * DOCUMENT ME! - * - * @param e DOCUMENT ME! + * + * @param e + * DOCUMENT ME! */ public void sortIDMenuItem_actionPerformed(ActionEvent e) { - SequenceI [] oldOrder = viewport.getAlignment().getSequencesArray(); + SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray(); AlignmentSorter.sortByID(viewport.getAlignment()); addHistoryItem(new OrderCommand("ID Sort", oldOrder, viewport.alignment)); alignPanel.paintAlignment(true); @@ -2874,42 +3362,60 @@ public class AlignFrame /** * DOCUMENT ME! - * - * @param e DOCUMENT ME! + * + * @param e + * DOCUMENT ME! + */ + public void sortLengthMenuItem_actionPerformed(ActionEvent e) + { + SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray(); + AlignmentSorter.sortByLength(viewport.getAlignment()); + addHistoryItem(new OrderCommand("Length Sort", oldOrder, + viewport.alignment)); + alignPanel.paintAlignment(true); + } + + /** + * DOCUMENT ME! + * + * @param e + * DOCUMENT ME! */ public void sortGroupMenuItem_actionPerformed(ActionEvent e) { - SequenceI [] oldOrder = viewport.getAlignment().getSequencesArray(); + SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray(); AlignmentSorter.sortByGroup(viewport.getAlignment()); - addHistoryItem(new OrderCommand("Group Sort", oldOrder, viewport.alignment)); + addHistoryItem(new OrderCommand("Group Sort", oldOrder, + viewport.alignment)); alignPanel.paintAlignment(true); } + /** * DOCUMENT ME! - * - * @param e DOCUMENT ME! + * + * @param e + * DOCUMENT ME! */ public void removeRedundancyMenuItem_actionPerformed(ActionEvent e) { new RedundancyPanel(alignPanel, this); } - /** * DOCUMENT ME! - * - * @param e DOCUMENT ME! + * + * @param e + * DOCUMENT ME! */ public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e) { - if ( (viewport.getSelectionGroup() == null) || - (viewport.getSelectionGroup().getSize() < 2)) + if ((viewport.getSelectionGroup() == null) + || (viewport.getSelectionGroup().getSize() < 2)) { JOptionPane.showInternalMessageDialog(this, - "You must select at least 2 sequences.", - "Invalid Selection", - JOptionPane.WARNING_MESSAGE); + "You must select at least 2 sequences.", "Invalid Selection", + JOptionPane.WARNING_MESSAGE); } else { @@ -2921,45 +3427,53 @@ public class AlignFrame /** * DOCUMENT ME! - * - * @param e DOCUMENT ME! + * + * @param e + * DOCUMENT ME! */ public void PCAMenuItem_actionPerformed(ActionEvent e) { - if ( ( (viewport.getSelectionGroup() != null) && - (viewport.getSelectionGroup().getSize() < 4) && - (viewport.getSelectionGroup().getSize() > 0)) || - (viewport.getAlignment().getHeight() < 4)) + if (((viewport.getSelectionGroup() != null) + && (viewport.getSelectionGroup().getSize() < 4) && (viewport + .getSelectionGroup().getSize() > 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); + "Principal component analysis must take\n" + + "at least 4 input sequences.", + "Sequence selection insufficient", + JOptionPane.WARNING_MESSAGE); return; } - new PCAPanel(alignPanel); + new PCAPanel(alignPanel); } - public void autoCalculate_actionPerformed(ActionEvent e) { viewport.autoCalculateConsensus = autoCalculate.isSelected(); - if(viewport.autoCalculateConsensus) + if (viewport.autoCalculateConsensus) { - viewport.firePropertyChange("alignment", - null, - viewport.getAlignment().getSequences()); + viewport.firePropertyChange("alignment", null, viewport + .getAlignment().getSequences()); } } + 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! + * + * @param e + * DOCUMENT ME! */ public void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e) { @@ -2968,8 +3482,9 @@ public class AlignFrame /** * DOCUMENT ME! - * - * @param e DOCUMENT ME! + * + * @param e + * DOCUMENT ME! */ public void neighbourTreeMenuItem_actionPerformed(ActionEvent e) { @@ -2978,8 +3493,9 @@ public class AlignFrame /** * DOCUMENT ME! - * - * @param e DOCUMENT ME! + * + * @param e + * DOCUMENT ME! */ protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e) { @@ -2988,8 +3504,9 @@ public class AlignFrame /** * DOCUMENT ME! - * - * @param e DOCUMENT ME! + * + * @param e + * DOCUMENT ME! */ protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e) { @@ -2998,10 +3515,13 @@ public class AlignFrame /** * DOCUMENT ME! - * - * @param type DOCUMENT ME! - * @param pwType DOCUMENT ME! - * @param title DOCUMENT ME! + * + * @param type + * DOCUMENT ME! + * @param pwType + * DOCUMENT ME! + * @param title + * DOCUMENT ME! */ void NewTreePanel(String type, String pwType, String title) { @@ -3011,10 +3531,11 @@ public class AlignFrame { if (viewport.getSelectionGroup().getSize() < 3) { - JOptionPane.showMessageDialog(Desktop.desktop, - "You need to have more than two sequences selected to build a tree!", - "Not enough sequences", - JOptionPane.WARNING_MESSAGE); + JOptionPane + .showMessageDialog( + Desktop.desktop, + "You need to have more than two sequences selected to build a tree!", + "Not enough sequences", JOptionPane.WARNING_MESSAGE); return; } @@ -3024,15 +3545,17 @@ public class AlignFrame /* Decide if the selection is a column region */ while (s < sg.getSize()) { - if ( ( (SequenceI) sg.getSequences(null).elementAt(s++)).getLength() < - sg.getEndRes()) + if (((SequenceI) sg.getSequences(null).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); + 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; } @@ -3043,20 +3566,22 @@ public class AlignFrame } else { - //are the sequences aligned? - if (!viewport.alignment.isAligned()) + // are the visible sequences aligned? + if (!viewport.alignment.isAligned(false)) { - 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); + 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; } - if(viewport.alignment.getHeight()<2) + if (viewport.alignment.getHeight() < 2) { return; } @@ -3066,9 +3591,9 @@ public class AlignFrame title += " from "; - if(viewport.viewName!=null) + if (viewport.viewName != null) { - title+= viewport.viewName+" of "; + title += viewport.viewName + " of "; } title += this.title; @@ -3078,11 +3603,14 @@ public class AlignFrame /** * DOCUMENT ME! - * - * @param title DOCUMENT ME! - * @param order DOCUMENT ME! + * + * @param title + * DOCUMENT ME! + * @param order + * DOCUMENT ME! */ - public void addSortByOrderMenuItem(String title, final AlignmentOrder order) + public void addSortByOrderMenuItem(String title, + final AlignmentOrder order) { final JMenuItem item = new JMenuItem("by " + title); sort.add(item); @@ -3090,24 +3618,31 @@ public class AlignFrame { public void actionPerformed(ActionEvent e) { - SequenceI [] oldOrder = viewport.getAlignment().getSequencesArray(); + SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray(); - // TODO: JBPNote - have to map order entries to curent SequenceI pointers + // TODO: JBPNote - have to map order entries to curent SequenceI + // pointers AlignmentSorter.sortBy(viewport.getAlignment(), order); addHistoryItem(new OrderCommand(order.getName(), oldOrder, - viewport.alignment)); + viewport.alignment)); 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 + * + * @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) + public void addSortByAnnotScoreMenuItem(JMenu sort, + final String scoreLabel) { final JMenuItem item = new JMenuItem(scoreLabel); sort.add(item); @@ -3115,43 +3650,48 @@ public class AlignFrame { public void actionPerformed(ActionEvent e) { - SequenceI [] oldOrder = viewport.getAlignment().getSequencesArray(); - AlignmentSorter.sortByAnnotationScore(scoreLabel, viewport.getAlignment()); - addHistoryItem(new OrderCommand("Sort by "+scoreLabel, oldOrder, viewport.alignment)); + SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray(); + AlignmentSorter.sortByAnnotationScore(scoreLabel, + viewport.getAlignment());// ,viewport.getSelectionGroup()); + addHistoryItem(new OrderCommand("Sort by " + scoreLabel, oldOrder, + viewport.alignment)); alignPanel.paintAlignment(true); } }); } + /** - * last hash for alignment's annotation array - used to minimise cost of rebuild. + * 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. - * + * 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. + * */ public void buildSortByAnnotationScoresMenu() { - if(viewport.alignment.getAlignmentAnnotation()==null) + if (viewport.alignment.getAlignmentAnnotation() == null) { return; } - if (viewport.alignment.getAlignmentAnnotation().hashCode()!=_annotationScoreVectorHash) + if (viewport.alignment.getAlignmentAnnotation().hashCode() != _annotationScoreVectorHash) { sortByAnnotScore.removeAll(); // almost certainly a quicker way to do this - but we keep it simple - Hashtable scoreSorts=new Hashtable(); + Hashtable scoreSorts = new Hashtable(); AlignmentAnnotation aann[]; Enumeration sq = viewport.alignment.getSequences().elements(); while (sq.hasMoreElements()) { aann = ((SequenceI) sq.nextElement()).getAnnotation(); - for (int i=0;aann!=null && i0); + sortByAnnotScore.setVisible(scoreSorts.size() > 0); scoreSorts.clear(); - _annotationScoreVectorHash = - viewport.alignment.getAlignmentAnnotation().hashCode(); + _annotationScoreVectorHash = viewport.alignment + .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. + * 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. */ public void buildTreeMenu() { sortByTreeMenu.removeAll(); - Vector comps = (Vector) PaintRefresher.components.get(viewport. - getSequenceSetId()); + Vector comps = (Vector) PaintRefresher.components.get(viewport + .getSequenceSetId()); Vector treePanels = new Vector(); int i, iSize = comps.size(); - for(i=0; i 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); - } */ + 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 { - /*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); - } - }*/ + /* + * 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); } } + */ msa = viewport.getAlignmentView(false); } 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). + * 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). */ - AlignmentView gatherSeqOrMsaForSecStrPrediction() + public AlignmentView gatherSeqOrMsaForSecStrPrediction() { - AlignmentView seqs = null; + AlignmentView seqs = null; - if ( (viewport.getSelectionGroup() != null) && - (viewport.getSelectionGroup().getSize() > 0)) + if ((viewport.getSelectionGroup() != null) + && (viewport.getSelectionGroup().getSize() > 0)) { seqs = viewport.getAlignmentView(true); } @@ -3290,26 +3840,32 @@ public class AlignFrame { seqs = viewport.getAlignmentView(false); } - // limit sequences - JBPNote in future - could spawn multiple prediction jobs - // TODO: viewport.alignment.isAligned is a global state - the local selection may well be aligned - we preserve 2.0.8 behaviour for moment. - if (!viewport.alignment.isAligned()) + // limit sequences - JBPNote in future - could spawn multiple prediction + // jobs + // TODO: viewport.alignment.isAligned is a global state - the local + // selection may well be aligned - we preserve 2.0.8 behaviour for moment. + if (!viewport.alignment.isAligned(false)) { seqs.setSequences(new SeqCigar[] - {seqs.getSequences()[0]}); + { seqs.getSequences()[0] }); + // TODO: if seqs.getSequences().length>1 then should really have warned + // user! + } return seqs; } + /** * DOCUMENT ME! - * - * @param e 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")); + 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"); @@ -3320,56 +3876,65 @@ public class AlignFrame { String choice = chooser.getSelectedFile().getPath(); jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice); - + jalview.io.NewickFile fin = null; try { - jalview.io.NewickFile fin = new jalview.io.NewickFile(choice, - "File"); + fin = new jalview.io.NewickFile(choice, "File"); viewport.setCurrentTree(ShowNewickTree(fin, choice).getTree()); + } catch (Exception ex) + { + JOptionPane.showMessageDialog(Desktop.desktop, ex.getMessage(), + "Problem reading tree file", JOptionPane.WARNING_MESSAGE); + ex.printStackTrace(); } - catch (Exception ex) + if (fin != null && fin.hasWarningMessage()) { JOptionPane.showMessageDialog(Desktop.desktop, - "Problem reading tree file", - ex.getMessage(), - JOptionPane.WARNING_MESSAGE); - ex.printStackTrace(); + fin.getWarningMessage(), "Possible problem with tree file", + JOptionPane.WARNING_MESSAGE); } } } - public TreePanel ShowNewickTree(NewickFile nf, String title) { - return ShowNewickTree(nf,title,600,500,4,5); + return ShowNewickTree(nf, title, 600, 500, 4, 5); } public TreePanel ShowNewickTree(NewickFile nf, String title, - AlignmentView input) + AlignmentView input) { - return ShowNewickTree(nf,title, input, 600,500,4,5); + return ShowNewickTree(nf, title, input, 600, 500, 4, 5); } - public TreePanel ShowNewickTree(NewickFile nf, String title, int w, int h, - int x, int y) + 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 + * 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) + AlignmentView input, int w, int h, int x, int y) { TreePanel tp = null; @@ -3379,23 +3944,18 @@ public class AlignFrame if (nf.getTree() != null) { - tp = new TreePanel(alignPanel, - "FromFile", - title, - nf, input); + tp = new TreePanel(alignPanel, "FromFile", title, nf, input); - tp.setSize(w,h); + tp.setSize(w, h); - if(x>0 && y>0) + if (x > 0 && y > 0) { - tp.setLocation(x,y); + tp.setLocation(x, y); } - Desktop.addInternalFrame(tp, title, w, h); } - } - catch (Exception ex) + } catch (Exception ex) { ex.printStackTrace(); } @@ -3403,206 +3963,277 @@ public class AlignFrame return tp; } + private boolean buildingMenu = false; /** * Generates menu items and listener event actions for web service clients - * + * */ public void BuildWebServiceMenu() { - if ( (Discoverer.services != null) - && (Discoverer.services.size() > 0)) + 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() { - Vector msaws = (Vector) Discoverer.services.get("MsaWS"); - Vector secstrpr = (Vector) Discoverer.services.get("SecStrPred"); - Vector wsmenu = new Vector(); - final AlignFrame af = this; - if (msaws != null) + public void run() { - // Add any Multiple Sequence Alignment Services - final JMenu msawsmenu = new JMenu("Alignment"); - for (int i = 0, j = msaws.size(); i < j; i++) + try { - final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle) msaws. - get(i); - final JMenuItem method = new JMenuItem(sh.getName()); - method.addActionListener(new ActionListener() + 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"); + // 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)) { - public void actionPerformed(ActionEvent e) + // TODO: refactor to allow list of AbstractName/Handler bindings to + // be + // stored or retrieved from elsewhere + Vector msaws = null; // (Vector) Discoverer.services.get("MsaWS"); + Vector secstrpr = (Vector) Discoverer.services + .get("SecStrPred"); + Vector seqsrch = null; // (Vector) Discoverer.services.get("SeqSearch"); + // TODO: move GUI generation code onto service implementation - so a + // client instance attaches itself to the GUI with method call like + // jalview.ws.MsaWSClient.bind(servicehandle, Desktop.instance, + // alignframe) + if (msaws != null) { - AlignmentView msa = gatherSequencesForAlignment(); - new jalview.ws.MsaWSClient(sh, title, msa, - false, true, - viewport.getAlignment().getDataset(), - af); + // Add any Multiple Sequence Alignment Services + for (int i = 0, j = msaws.size(); i < j; i++) + { + final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle) msaws + .get(i); + jalview.ws.WSMenuEntryProviderI impl = jalview.ws.jws1.Discoverer + .getServiceClient(sh); + impl.attachWSMenuEntry(msawsmenu, me); + } } - - }); - 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() + if (secstrpr != null) { - public void actionPerformed(ActionEvent e) + // Add any secondary structure prediction services + for (int i = 0, j = secstrpr.size(); i < j; i++) { - AlignmentView msa = gatherSequencesForAlignment(); - new jalview.ws.MsaWSClient(sh, title, msa, - true, true, - viewport.getAlignment().getDataset(), - af); - + final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle) secstrpr + .get(i); + jalview.ws.WSMenuEntryProviderI impl = jalview.ws.jws1.Discoverer + .getServiceClient(sh); + impl.attachWSMenuEntry(secstrmenu, me); } - - }); - msawsmenu.add(methodR); - + } + if (seqsrch != null) + { + // Add any sequence search services + for (int i = 0, j = seqsrch.size(); i < j; i++) + { + final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle) seqsrch + .elementAt(i); + jalview.ws.WSMenuEntryProviderI impl = jalview.ws.jws1.Discoverer + .getServiceClient(sh); + impl.attachWSMenuEntry(seqsrchmenu, me); + } + } } - } - 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() + + // TODO: move into separate menu builder class. + if (Cache.getDefault("SHOW_JWS2_SERVICES", true)) { - public void actionPerformed(ActionEvent e) + Jws2Discoverer jws2servs = Jws2Discoverer.getDiscoverer(); + if (jws2servs != null) { - AlignmentView msa = gatherSeqOrMsaForSecStrPrediction(); - if (msa.getSequences().length == 1) + if (jws2servs.hasServices()) { - // Single Sequence prediction - new jalview.ws.JPredClient(sh, title, false, msa, af, true); + jws2servs.attachWSMenuEntry(msawsmenu, me); } - else + } + } + // Add all submenus in the order they should appear on the web services menu + wsmenu.add(msawsmenu); + wsmenu.add(secstrmenu); + wsmenu.add(analymenu); + // No search services yet + // wsmenu.add(seqsrchmenu); + + javax.swing.SwingUtilities.invokeLater(new Runnable() + { + public void run() + { + try { - if (msa.getSequences().length > 1) + webService.removeAll(); + // first, add discovered services onto the webservices menu + if (wsmenu.size() > 0) { - // Sequence profile based prediction - new jalview.ws.JPredClient(sh, - title, true, msa, af, true); + for (int i = 0, j = wsmenu.size(); i < j; i++) + { + webService.add((JMenu) wsmenu.get(i)); + } + } + else + { + webService.add(me.webServiceNoServices); } + build_urlServiceMenu(me.webService); + build_fetchdbmenu(webService); + } catch (Exception e) + { } + ; } }); - secstrmenu.add(method); + } catch (Exception e) + { } - wsmenu.add(secstrmenu); - } - resetWebServiceMenu(); - for (int i = 0, j = wsmenu.size(); i < j; i++) - { - webService.add( (JMenu) wsmenu.get(i)); + ; + + buildingMenu = false; } - } - else - { - resetWebServiceMenu(); - this.webService.add(this.webServiceNoServices); - } - // TODO: add in rediscovery function - // TODO: reduce code redundancy. - // TODO: group services by location as well as function. + }).start(); + } /** - * empty the web service menu and add any ad-hoc functions - * not dynamically discovered. - * + * construct any groupURL type service menu entries. + * + * @param webService */ - private void resetWebServiceMenu() + private void build_urlServiceMenu(JMenu webService) { - webService.removeAll(); - // Temporary hack - DBRef Fetcher always top level ws entry. - JMenuItem rfetch = new JMenuItem("Fetch DB References"); - rfetch.setToolTipText("Retrieve and parse uniprot records for the alignment or the currently selected sequences"); - webService.add(rfetch); - rfetch.addActionListener(new ActionListener() { - - public void actionPerformed(ActionEvent e) - { - new jalview.ws.DBRefFetcher( - alignPanel.av.getSequenceSelection(), - alignPanel.alignFrame).fetchDBRefs(false); - } - - }); - } - - /* 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); + // 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.alignment, + * af.viewport.colSel, 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); + } - if (value == JalviewFileChooser.APPROVE_OPTION) + if (Cache.getDefault("SHOW_ENFIN_SERVICES", true)) { - jalview.io.VamsasDatastore vs = new jalview.io.VamsasDatastore(viewport); - //vs.store(chooser.getSelectedFile().getAbsolutePath() ); - vs.storeJalview( chooser.getSelectedFile().getAbsolutePath(), this); + jalview.ws.EnfinEnvision2OneWay.getInstance().attachWSMenuEntry( + webService, this); } - }*/ + } + + /* + * 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(chooser.getSelectedFile().getAbsolutePath() ); vs.storeJalview( + * chooser.getSelectedFile().getAbsolutePath(), this); } } + */ /** * prototype of an automatically enabled/disabled analysis function - * + * */ protected void setShowProductsEnabled() { - SequenceI [] selection = viewport.getSequenceSelection(); - if (canShowProducts(selection, viewport.getSelectionGroup()!=null, viewport.getAlignment().getDataset())) + SequenceI[] selection = viewport.getSequenceSelection(); + if (canShowProducts(selection, viewport.getSelectionGroup() != null, + viewport.getAlignment().getDataset())) { showProducts.setEnabled(true); - - } else { + + } + else + { showProducts.setEnabled(false); } } + /** - * search selection for sequence xRef products and build the - * show products menu. + * search selection for sequence xRef products and build the show products + * menu. + * * @param selection * @param dataset * @return true if showProducts menu should be enabled. */ - public boolean canShowProducts(SequenceI[] selection, boolean isRegionSelection, Alignment dataset) + public boolean canShowProducts(SequenceI[] selection, + boolean isRegionSelection, Alignment dataset) { - boolean showp=false; - try { + boolean showp = false; + try + { showProducts.removeAll(); final boolean dna = viewport.getAlignment().isNucleotide(); final Alignment ds = dataset; - String[] ptypes = CrossRef.findSequenceXrefTypes(dna, selection, dataset); - //Object[] prods = CrossRef.buildXProductsList(viewport.getAlignment().isNucleotide(), selection, dataset, true); + String[] ptypes = (selection == null || selection.length == 0) ? null + : CrossRef.findSequenceXrefTypes(dna, selection, dataset); + // Object[] prods = + // CrossRef.buildXProductsList(viewport.getAlignment().isNucleotide(), + // selection, dataset, true); final SequenceI[] sel = selection; - for (int t=0; ptypes!=null && t filesmatched = new ArrayList(); + ArrayList filesnotmatched = new ArrayList(); for (int i = 0; i < files.size(); i++) { - loadJalviewDataFile(files.get(i).toString()); + 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); + } } - } - catch (Exception ex) + int assocfiles = 0; + if (filesmatched.size() > 0) + { + if (Cache.getDefault("AUTOASSOCIATE_PDBANDSEQS", false) + || JOptionPane + .showConfirmDialog( + this, + "Do you want to automatically associate the " + + filesmatched.size() + + " PDB files with sequences in the alignment that have the same name ?", + "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); + 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, + "Do you want to ignore the " + + filesnotmatched.size() + + " files whose names did not match any sequence IDs ?", + "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(); } } -} + } - // This method will attempt to load a "dropped" file first by testing - // whether its and Annotation file, then features file. If both are - // false then the user may have dropped an alignment file onto this - // AlignFrame - public void loadJalviewDataFile(String file) + /** + * Attempt to load a "dropped" file or URL string: First by testing whether + * it's and 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 { - String protocol = "File"; - - if (file.indexOf("http:") > -1 || file.indexOf("file:") > -1) + if (protocol == null) { - protocol = "URL"; + protocol = jalview.io.FormatAdapter.checkProtocol(file); } - - boolean isAnnotation = new AnnotationFile().readAnnotationFile(viewport. - alignment, file, protocol); + // 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() + .readAnnotationFile(viewport.alignment, file, protocol) + : false; if (!isAnnotation) { - boolean isGroupsFile = parseFeaturesFile(file,protocol); - if (!isGroupsFile) + // try to see if its a JNet 'concise' style annotation file *before* we + // try to parse it as a features file + if (format == null) { - String format = new IdentifyFile().Identify(file, protocol); - - if(format.equalsIgnoreCase("JnetFile")) + format = new IdentifyFile().Identify(file, protocol); + } + if (format.equalsIgnoreCase("JnetFile")) + { + jalview.io.JPredFile predictions = new jalview.io.JPredFile(file, + protocol); + new JnetAnnotationMaker().add_annotation(predictions, + viewport.getAlignment(), 0, false); + isAnnotation = true; + } + else + { + /* + * if (format.equalsIgnoreCase("PDB")) { + * + * String pdbfn = ""; // try to match up filename with sequence id try + * { 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(); } } catch (Exception e) { } ; if (assocSeq == null) + * { SequenceIdMatcher idm = new SequenceIdMatcher(viewport + * .getAlignment().getSequencesArray()); if (pdbfn.length() > 0) { // + * attempt to find a match in the alignment SequenceI mtch = + * idm.findIdMatch(pdbfn); int l = 0, c = pdbfn.indexOf("."); while + * (mtch == null && c != -1) { while ((c = pdbfn.indexOf(".", l)) > l) + * { l = c; } if (l > -1) { pdbfn = pdbfn.substring(0, l); } mtch = + * idm.findIdMatch(pdbfn); } if (mtch != null) { // try and associate + * // prompt ? PDBEntry pe = new AssociatePdbFileWithSeq() + * .associatePdbWithSeq(file, protocol, mtch, true); if (pe != null) { + * System.err.println("Associated file : " + file + " with " + + * mtch.getDisplayId(true)); alignPanel.paintAlignment(true); } } // + * TODO: maybe need to load as normal otherwise return; } } + */ + // try to parse it as a features file + boolean isGroupsFile = parseFeaturesFile(file, protocol); + // if it wasn't a features file then we just treat it as a general + // alignment file to load into the current view. + if (!isGroupsFile) { - jalview.io.JPredFile predictions = new jalview.io.JPredFile( - file, protocol); - new JnetAnnotationMaker().add_annotation(predictions, - viewport.getAlignment(), - 0, false); - alignPanel.adjustAnnotationHeight(); - alignPanel.paintAlignment(true); + new FileLoader().LoadFile(viewport, file, protocol, format); } else { - new FileLoader().LoadFile(viewport, file, protocol, format); + alignPanel.paintAlignment(true); + } } } - } - else + if (isAnnotation) { - // (isAnnotation) + alignPanel.adjustAnnotationHeight(); + viewport.updateSequenceIdColours(); buildSortByAnnotationScoresMenu(); + alignPanel.paintAlignment(true); } - - } - catch (Exception ex) + } catch (Exception ex) { ex.printStackTrace(); } @@ -3888,50 +4759,365 @@ public void drop(DropTargetDropEvent evt) public void tabbedPane_mousePressed(MouseEvent e) { - if(SwingUtilities.isRightMouseButton(e)) + if (SwingUtilities.isRightMouseButton(e)) { String reply = JOptionPane.showInternalInputDialog(this, - "Enter View Name", - "Edit View Name", - JOptionPane.QUESTION_MESSAGE); + "Enter View Name", "Edit View Name", + JOptionPane.QUESTION_MESSAGE); if (reply != null) { viewport.viewName = reply; - tabbedPane.setTitleAt( tabbedPane.getSelectedIndex() ,reply); + tabbedPane.setTitleAt(tabbedPane.getSelectedIndex(), reply); } } } - public AlignViewport getCurrentView() { return viewport; } - /** * Open the dialog for regex description parsing. */ protected void extractScores_actionPerformed(ActionEvent e) { - ParseProperties pp = new jalview.analysis.ParseProperties(viewport.alignment); - if (pp.getScoresFromDescription("col", "score column ", "\\W+([-+]?\\d*\\.?\\d*e?-?\\d*)\\W+([-+]?\\d*\\.?\\d*e?-?\\d*)")>0) + ParseProperties pp = new jalview.analysis.ParseProperties( + viewport.alignment); + // 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 + * ) + */ + protected void showDbRefs_actionPerformed(ActionEvent e) + { + viewport.setShowDbRefs(showDbRefsMenuitem.isSelected()); + } + + /* + * (non-Javadoc) + * + * @seejalview.jbgui.GAlignFrame#showNpFeats_actionPerformed(java.awt.event. + * ActionEvent) + */ + 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(AlignViewport 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("Fetch DB References"); + rfetch.setToolTipText("Retrieve and parse sequence database records for the alignment or the currently selected sequences"); + webService.add(rfetch); + + JMenuItem fetchr = new JMenuItem("Standard Databases"); + fetchr.setToolTipText("Fetch from EMBL/EMBLCDS or Uniprot/PDB and any selected DAS sources"); + fetchr.addActionListener(new ActionListener() + { + + public void actionPerformed(ActionEvent e) + { + new Thread(new Runnable() + { + + public void run() + { + new jalview.ws.DBRefFetcher(alignPanel.av + .getSequenceSelection(), alignPanel.alignFrame) + .fetchDBRefs(false); + } + }).start(); + + } + + }); + rfetch.add(fetchr); + final AlignFrame me = this; + new Thread(new Runnable() + { + public void run() + { + final jalview.ws.SequenceFetcher sf = SequenceFetcher + .getSequenceFetcherSingleton(me); + final String[] otherdb = sf.getOrderedSupportedSources(); + // sf.getDbInstances(jalview.ws.dbsources.DasSequenceSource.class); + // jalview.util.QuickSort.sort(otherdb, otherdb); + javax.swing.SwingUtilities.invokeLater(new Runnable() + { + public void run() + { + + JMenu dfetch = new JMenu(); + JMenuItem fetchr; + rfetch.add(dfetch); + int comp = 0, mcomp = 15; + String mname = null; + if (otherdb != null && otherdb.length > 0) + { + for (int i = 0; i < otherdb.length; i++) + { + String dbname = sf.getSourceProxy(otherdb[i]).getDbName(); + if (mname == null) + { + mname = "from '" + dbname + "'"; + } + fetchr = new JMenuItem(otherdb[i]); + final String[] dassource = new String[] + { otherdb[i] }; + fetchr.addActionListener(new ActionListener() + { + + public void actionPerformed(ActionEvent e) + { + new Thread(new Runnable() + { + + public void run() + { + new jalview.ws.DBRefFetcher(alignPanel.av + .getSequenceSelection(), + alignPanel.alignFrame, dassource) + .fetchDBRefs(false); + } + }).start(); + } + + }); + fetchr.setToolTipText("Retrieve from " + dbname); + dfetch.add(fetchr); + if (comp++ == mcomp || i == (otherdb.length - 1)) + { + dfetch.setText(mname + " to '" + dbname + "'"); + rfetch.add(dfetch); + dfetch = new JMenu(); + mname = null; + comp = 0; + } + } + } + } + }); + } + }).start(); + + } + + /** + * Left justify the whole alignment. + */ + protected void justifyLeftMenuItem_actionPerformed(ActionEvent e) + { + AlignmentI al = viewport.getAlignment(); + al.justify(false); + viewport.firePropertyChange("alignment", null, al); + } + + /** + * Right justify the whole alignment. + */ + protected void justifyRightMenuItem_actionPerformed(ActionEvent e) + { + AlignmentI al = viewport.getAlignment(); + al.justify(true); + viewport.firePropertyChange("alignment", null, al); + } + + public void setShowSeqFeatures(boolean b) + { + showSeqFeatures.setSelected(true); + viewport.setShowSequenceFeatures(true); + } + + /* + * (non-Javadoc) + * + * @see + * jalview.jbgui.GAlignFrame#showUnconservedMenuItem_actionPerformed(java. + * awt.event.ActionEvent) + */ + 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) + */ + 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) + */ + 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) + */ + 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) + */ + protected void showSequenceLogo_actionPerformed(ActionEvent e) + { + viewport.setShowSequenceLogo(showSequenceLogo.getState()); + alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState()); + } + + protected void applyAutoAnnotationSettings_actionPerformed(ActionEvent e) + { + alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState()); + } + + /* + * (non-Javadoc) + * + * @see + * jalview.jbgui.GAlignFrame#makeGrpsFromSelection_actionPerformed(java.awt + * .event.ActionEvent) + */ + protected void makeGrpsFromSelection_actionPerformed(ActionEvent e) + { + if (viewport.getSelectionGroup() != null) + { + SequenceGroup[] gps = jalview.analysis.Grouping.makeGroupsFrom( + viewport.getSequenceSelection(), + viewport.getAlignmentView(true).getSequenceStrings( + viewport.getGapCharacter()), + viewport.alignment.getGroups()); + viewport.alignment.deleteAllGroups(); + viewport.sequenceColours = null; + viewport.setSelectionGroup(null); + // set view properties for each group + for (int g = 0; g < gps.length; g++) + { + gps[g].setShowNonconserved(viewport.getShowUnconserved()); + gps[g].setshowSequenceLogo(viewport.isShowSequenceLogo()); + viewport.alignment.addGroup(gps[g]); + Color col = new Color((int) (Math.random() * 255), + (int) (Math.random() * 255), (int) (Math.random() * 255)); + col = col.brighter(); + for (Enumeration sq = gps[g].getSequences(null).elements(); sq + .hasMoreElements(); viewport.setSequenceColour( + (SequenceI) sq.nextElement(), col)) + ; + } + PaintRefresher.Refresh(this, viewport.getSequenceSetId()); + alignPanel.updateAnnotation(); + alignPanel.paintAlignment(true); + } + } + + /** + * 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( + "Implementation error: cannot show a view from another alignment in an AlignFrame."); + } + if (tabbedPane != null + & alignPanels.indexOf(alignmentPanel) != tabbedPane.getSelectedIndex()) + { + tabbedPane.setSelectedIndex(alignPanels.indexOf(alignmentPanel)); + } + } } -class PrintThread - extends Thread +class PrintThread extends Thread { AlignmentPanel ap; + public PrintThread(AlignmentPanel ap) { - this.ap = ap; + this.ap = ap; } + static PageFormat pf; + public void run() { PrinterJob printJob = PrinterJob.getPrinterJob(); @@ -3950,8 +5136,7 @@ class PrintThread try { printJob.print(); - } - catch (Exception PrintException) + } catch (Exception PrintException) { PrintException.printStackTrace(); }