X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FAlignFrame.java;h=e51131b4a893ff2a2c370848b42cdf040ff21f2f;hb=dfa39e09cf3ffa44cc1e764bfa72900bab96136d;hp=0f7ac3ec77dd9cbb2e6e66f6d243bd1e40505282;hpb=1f3240f018a6442b1116c409a624fba042cc9efd;p=jalview.git diff --git a/src/jalview/appletgui/AlignFrame.java b/src/jalview/appletgui/AlignFrame.java old mode 100755 new mode 100644 index 0f7ac3e..e51131b --- a/src/jalview/appletgui/AlignFrame.java +++ b/src/jalview/appletgui/AlignFrame.java @@ -1,78 +1,269 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer - * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle - * - * This program is free software; you can redistribute it and/or - * modify it under the terms of the GNU General Public License - * as published by the Free Software Foundation; either version 2 + * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$) + * Copyright (C) $$Year-Rel$$ The Jalview Authors + * + * This file is part of Jalview. + * + * Jalview is free software: you can redistribute it and/or + * modify it under the terms of the GNU General Public License + * as published by the Free Software Foundation, either version 3 * of the License, or (at your option) any later version. - * - * 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. - * + * + * 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 this program; if not, write to the Free Software - * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA + * along with Jalview. If not, see . + * The Jalview Authors are detailed in the 'AUTHORS' file. */ - package jalview.appletgui; -import jalview.schemes.*; -import jalview.datamodel.*; -import jalview.analysis.*; -import jalview.io.*; -import java.awt.*; -import java.awt.event.*; -import java.util.*; -import java.io.InputStreamReader; -import java.io.BufferedReader; +import jalview.analysis.AlignmentSorter; +import jalview.analysis.AnnotationSorter.SequenceAnnotationOrder; +import jalview.api.AlignViewControllerGuiI; +import jalview.api.AlignViewControllerI; +import jalview.api.AlignViewportI; +import jalview.api.FeatureColourI; +import jalview.api.FeatureRenderer; +import jalview.api.FeatureSettingsControllerI; +import jalview.api.SequenceStructureBinding; +import jalview.bin.JalviewLite; +import jalview.commands.CommandI; +import jalview.commands.EditCommand; +import jalview.commands.EditCommand.Action; +import jalview.commands.OrderCommand; +import jalview.commands.RemoveGapColCommand; +import jalview.commands.RemoveGapsCommand; +import jalview.commands.SlideSequencesCommand; +import jalview.commands.TrimRegionCommand; +import jalview.datamodel.Alignment; +import jalview.datamodel.AlignmentAnnotation; +import jalview.datamodel.AlignmentI; +import jalview.datamodel.AlignmentOrder; +import jalview.datamodel.ColumnSelection; +import jalview.datamodel.PDBEntry; +import jalview.datamodel.Sequence; +import jalview.datamodel.SequenceGroup; +import jalview.datamodel.SequenceI; +import jalview.io.AnnotationFile; +import jalview.io.AppletFormatAdapter; +import jalview.io.DataSourceType; +import jalview.io.FeaturesFile; +import jalview.io.FileFormat; +import jalview.io.FileFormatI; +import jalview.io.FileFormats; +import jalview.io.TCoffeeScoreFile; +import jalview.schemes.Blosum62ColourScheme; +import jalview.schemes.BuriedColourScheme; +import jalview.schemes.ClustalxColourScheme; +import jalview.schemes.ColourSchemeI; +import jalview.schemes.HelixColourScheme; +import jalview.schemes.HydrophobicColourScheme; +import jalview.schemes.NucleotideColourScheme; +import jalview.schemes.PIDColourScheme; +import jalview.schemes.PurinePyrimidineColourScheme; +import jalview.schemes.RNAHelicesColour; +import jalview.schemes.StrandColourScheme; +import jalview.schemes.TCoffeeColourScheme; +import jalview.schemes.TaylorColourScheme; +import jalview.schemes.TurnColourScheme; +import jalview.schemes.ZappoColourScheme; +import jalview.structure.StructureSelectionManager; +import jalview.structures.models.AAStructureBindingModel; +import jalview.util.MappingUtils; +import jalview.util.MessageManager; +import jalview.viewmodel.AlignmentViewport; +import jalview.viewmodel.ViewportRanges; + +import java.awt.BorderLayout; +import java.awt.Canvas; +import java.awt.CheckboxMenuItem; +import java.awt.Color; +import java.awt.FlowLayout; +import java.awt.Font; +import java.awt.FontMetrics; +import java.awt.Frame; +import java.awt.Graphics; +import java.awt.Label; +import java.awt.Menu; +import java.awt.MenuBar; +import java.awt.MenuItem; +import java.awt.Panel; +import java.awt.event.ActionEvent; +import java.awt.event.ActionListener; +import java.awt.event.FocusEvent; +import java.awt.event.FocusListener; +import java.awt.event.ItemEvent; +import java.awt.event.ItemListener; +import java.awt.event.KeyEvent; +import java.awt.event.KeyListener; +import java.awt.event.WindowAdapter; +import java.awt.event.WindowEvent; +import java.io.IOException; import java.net.URL; - - -public class AlignFrame extends Frame implements ActionListener, - ItemListener, KeyListener, MouseListener +import java.net.URLEncoder; +import java.util.Arrays; +import java.util.Deque; +import java.util.HashMap; +import java.util.List; +import java.util.Map; +import java.util.StringTokenizer; +import java.util.Vector; + +import org.jmol.viewer.Viewer; + +public class AlignFrame extends EmbmenuFrame implements ActionListener, + ItemListener, KeyListener, AlignViewControllerGuiI { + public AlignViewControllerI avc; + public AlignmentPanel alignPanel; + public AlignViewport viewport; - int NEW_WINDOW_WIDTH = 700; - int NEW_WINDOW_HEIGHT = 500; + + // width and height may be overridden by applet parameters + int frameWidth = 700; + + int frameHeight = 500; String jalviewServletURL; + /* + * Flag for showing autocalculated consensus above or below other consensus + * rows + */ + private boolean showAutoCalculatedAbove; + + private SequenceAnnotationOrder annotationSortOrder; + + /** + * Constructor that creates the frame and adds it to the display. + * + * @param al + * @param applet + * @param title + * @param embedded + */ + public AlignFrame(AlignmentI al, JalviewLite applet, String title, + boolean embedded) + { + this(al, applet, title, embedded, true); + } + + /** + * Constructor that optionally allows the frame to be displayed or only + * created. + * + * @param al + * @param applet + * @param title + * @param embedded + * @param addToDisplay + */ + public AlignFrame(AlignmentI al, JalviewLite applet, String title, + boolean embedded, boolean addToDisplay) + { + this(al, null, null, applet, title, embedded, addToDisplay); + } - public AlignFrame(AlignmentI al, - jalview.bin.JalviewLite applet, - String title, - boolean embedded) + public AlignFrame(AlignmentI al, SequenceI[] hiddenSeqs, + ColumnSelection columnSelection, JalviewLite applet, + String title, boolean embedded) { + this(al, hiddenSeqs, columnSelection, applet, title, embedded, true); + } - jalviewServletURL = applet.getParameter("APPLICATION_URL"); + public AlignFrame(AlignmentI al, SequenceI[] hiddenSeqs, + ColumnSelection columnSelection, JalviewLite applet, + String title, boolean embedded, boolean addToDisplay) + { + if (applet != null) + { + jalviewServletURL = applet.getParameter("APPLICATION_URL"); + } - try{ + try + { jbInit(); - }catch(Exception ex) + } catch (Exception ex) { ex.printStackTrace(); } - + // need to get window geometry before we calculate alignment layout + if (applet != null) + { + String param; + try + { + param = applet.getParameter("windowWidth"); + if (param != null) + { + int width = Integer.parseInt(param); + frameWidth = width; + } + param = applet.getParameter("windowHeight"); + if (param != null) + { + int height = Integer.parseInt(param); + frameHeight = height; + } + } catch (Exception ex) + { + } + } viewport = new AlignViewport(al, applet); - alignPanel = new AlignmentPanel(this, viewport); - - annotationPanelMenuItem.setState(viewport.showAnnotation); - seqLimits.setState(viewport.showJVSuffix); + if (hiddenSeqs != null && hiddenSeqs.length > 0) + { + viewport.hideSequence(hiddenSeqs); + } + if (columnSelection != null) + { + viewport.setColumnSelection(columnSelection); + } + viewport.setScaleAboveWrapped(scaleAbove.getState()); - if(applet!=null) + alignPanel = new AlignmentPanel(this, viewport); + avc = new jalview.controller.AlignViewController(this, viewport, + alignPanel); + viewport.updateConservation(alignPanel); + viewport.updateConsensus(alignPanel); + + displayNonconservedMenuItem.setState(viewport.getShowUnconserved()); + followMouseOverFlag.setState(viewport.isFollowHighlight()); + showGroupConsensus.setState(viewport.isShowGroupConsensus()); + showGroupConservation.setState(viewport.isShowGroupConservation()); + showConsensusHistogram.setState(viewport.isShowConsensusHistogram()); + showSequenceLogo.setState(viewport.isShowSequenceLogo()); + normSequenceLogo.setState(viewport.isNormaliseSequenceLogo()); + applyToAllGroups.setState(viewport.getColourAppliesToAllGroups()); + annotationPanelMenuItem.setState(viewport.isShowAnnotation()); + showAlignmentAnnotations.setEnabled(annotationPanelMenuItem.getState()); + showSequenceAnnotations.setEnabled(annotationPanelMenuItem.getState()); + showAlignmentAnnotations.setState(true); + showSequenceAnnotations.setState(false); + + seqLimits.setState(viewport.getShowJVSuffix()); + + if (applet != null) { String param = applet.getParameter("sortBy"); if (param != null) { if (param.equalsIgnoreCase("Id")) + { sortIDMenuItem_actionPerformed(); + } else if (param.equalsIgnoreCase("Pairwise Identity")) + { sortPairwiseMenuItem_actionPerformed(); + } + else if (param.equalsIgnoreCase("Length")) + { + sortLengthMenuItem_actionPerformed(); + } } param = applet.getParameter("wrap"); @@ -84,60 +275,73 @@ public class AlignFrame extends Frame implements ActionListener, wrapMenuItem_actionPerformed(); } } - - try + param = applet.getParameter("centrecolumnlabels"); + if (param != null) { - param = applet.getParameter("windowWidth"); - if (param != null) - { - int width = Integer.parseInt(param); - NEW_WINDOW_WIDTH = width; - } - param = applet.getParameter("windowHeight"); - if (param != null) - { - int height = Integer.parseInt(param); - NEW_WINDOW_HEIGHT = height; - } + centreColumnLabelFlag.setState(true); + centreColumnLabelFlag_stateChanged(); } - catch (Exception ex) - {} } - - //Some JVMS send keyevents to Top frame or lowest panel, - //Havent worked out why yet. So add to both this frame and seqCanvas for now - this.addKeyListener(this); - alignPanel.seqPanel.seqCanvas.addKeyListener(this); - alignPanel.idPanel.idCanvas.addKeyListener(this); - alignPanel.scalePanel.addKeyListener(this); - alignPanel.annotationPanel.addKeyListener(this); - - viewport.addPropertyChangeListener(new java.beans.PropertyChangeListener() + if (viewport.getAlignment().isNucleotide()) { - public void propertyChange(java.beans.PropertyChangeEvent evt) - { - if (evt.getPropertyName().equals("alignment")) - { - alignmentChanged(); - } - } - }); - + conservationMenuItem.setEnabled(false); + clustalColour.setEnabled(false); + BLOSUM62Colour.setEnabled(false); + zappoColour.setEnabled(false); + taylorColour.setEnabled(false); + hydrophobicityColour.setEnabled(false); + helixColour.setEnabled(false); + strandColour.setEnabled(false); + turnColour.setEnabled(false); + buriedColour.setEnabled(false); + viewport.updateStrucConsensus(alignPanel); + if (viewport.getAlignment().hasRNAStructure()) + { + RNAHelixColour.setEnabled(true); + } + else + { + RNAHelixColour.setEnabled(false); + } + } + else + { + RNAHelixColour.setEnabled(false); + purinePyrimidineColour.setEnabled(false); + nucleotideColour.setEnabled(false); + } + // Some JVMS send keyevents to Top frame or lowest panel, + // Havent worked out why yet. So add to both this frame and seqCanvas for + // now + this.addKeyListener(this); + alignPanel.seqPanel.seqCanvas.addKeyListener(this); + alignPanel.idPanel.idCanvas.addKeyListener(this); + alignPanel.scalePanel.addKeyListener(this); + alignPanel.annotationPanel.addKeyListener(this); + alignPanel.annotationPanelHolder.addKeyListener(this); + alignPanel.annotationSpaceFillerHolder.addKeyListener(this); + alignPanel.alabels.addKeyListener(this); + + setAnnotationsVisibility(); + + if (addToDisplay) + { + addToDisplay(embedded); + } + } - if(embedded) - { - setEmbedded(); - } - else - { - add(alignPanel, BorderLayout.CENTER); - jalview.bin.JalviewLite.addFrame(this, title, NEW_WINDOW_WIDTH, - NEW_WINDOW_HEIGHT); - } - alignPanel.validate(); - alignPanel.repaint(); + /** + * @param embedded + */ + public void addToDisplay(boolean embedded) + { + createAlignFrameWindow(embedded); + validate(); + alignPanel.adjustAnnotationHeight(); + alignPanel.paintAlignment(true); } + public AlignViewport getAlignViewport() { return viewport; @@ -148,2253 +352,3964 @@ public class AlignFrame extends Frame implements ActionListener, return alignPanel.seqPanel.seqCanvas; } - /** - * DOCUMENT ME! - * - * @param String DOCUMENT ME! + * Load a features file onto the alignment + * + * @param file + * file URL, content, or other resolvable path + * @param type + * is protocol for accessing data referred to by file */ - public void parseFeaturesFile(String file, String type) + public boolean parseFeaturesFile(String file, DataSourceType type) + { + return parseFeaturesFile(file, type, true); + } + + /** + * Load a features file onto the alignment + * + * @param file + * file URL, content, or other resolvable path + * @param sourceType + * is protocol for accessing data referred to by file + * @param autoenabledisplay + * when true, display features flag will be automatically enabled if + * features are loaded + * @return true if data parsed as a features file + */ + public boolean parseFeaturesFile(String file, DataSourceType sourceType, + boolean autoenabledisplay) { - Hashtable featureLinks = new Hashtable(); boolean featuresFile = false; - try{ - featuresFile = new jalview.io.FeaturesFile(file, type).parse(viewport.alignment, - alignPanel.seqPanel.seqCanvas. - getFeatureRenderer().featureColours, - featureLinks, - true); - } - catch(Exception ex) + try + { + Map colours = alignPanel.seqPanel.seqCanvas + .getFeatureRenderer().getFeatureColours(); + boolean relaxedIdMatching = viewport.applet.getDefaultParameter( + "relaxedidmatch", false); + featuresFile = new FeaturesFile(file, sourceType).parse( + viewport.getAlignment(), colours, true, relaxedIdMatching); + } catch (Exception ex) { ex.printStackTrace(); } - if(featuresFile) + if (featuresFile) { - if(featureLinks.size()>0) - alignPanel.seqPanel.seqCanvas - .getFeatureRenderer().featureLinks = featureLinks; - viewport.showSequenceFeatures = true; - sequenceFeatures.setState(true); - alignPanel.repaint(); + if (autoenabledisplay) + { + viewport.setShowSequenceFeatures(true); + sequenceFeatures.setState(true); + } + if (alignPanel.seqPanel.seqCanvas.fr != null) + { + // update the min/max ranges where necessary + alignPanel.seqPanel.seqCanvas.fr.findAllFeatures(true); + } + if (viewport.featureSettings != null) + { + viewport.featureSettings.refreshTable(); + } + alignPanel.paintAlignment(true); + statusBar.setText(MessageManager + .getString("label.successfully_added_features_alignment")); } - + return featuresFile; } - + @Override public void keyPressed(KeyEvent evt) { + ViewportRanges ranges = viewport.getRanges(); + if (viewport.cursorMode - && evt.getKeyCode() >= KeyEvent.VK_0 - && evt.getKeyCode() <= KeyEvent.VK_9) + && ((evt.getKeyCode() >= KeyEvent.VK_0 && evt.getKeyCode() <= KeyEvent.VK_9) || (evt + .getKeyCode() >= KeyEvent.VK_NUMPAD0 && evt + .getKeyCode() <= KeyEvent.VK_NUMPAD9)) + && Character.isDigit(evt.getKeyChar())) { alignPanel.seqPanel.numberPressed(evt.getKeyChar()); } switch (evt.getKeyCode()) { - case 27: // escape key - deselectAllSequenceMenuItem_actionPerformed(); - break; - case KeyEvent.VK_X: - if (evt.isControlDown() || evt.isMetaDown()) - { - cut_actionPerformed(); - } - break; - case KeyEvent.VK_C: - if (viewport.cursorMode && !evt.isControlDown()) - { - alignPanel.seqPanel.setCursorColumn(); - } - if (evt.isControlDown() || evt.isMetaDown()) - { - copy_actionPerformed(); - } - break; - case KeyEvent.VK_V: - if (evt.isControlDown() || evt.isMetaDown()) - { - paste(true); - } - break; - case KeyEvent.VK_A: - if (evt.isControlDown() || evt.isMetaDown()) - { - selectAllSequenceMenuItem_actionPerformed(); - } - break; - case KeyEvent.VK_DOWN: - if(viewport.cursorMode) - { - alignPanel.seqPanel.moveCursor(0,1); - } - else - moveSelectedSequences(false); - break; + case 27: // escape key + deselectAllSequenceMenuItem_actionPerformed(); - case KeyEvent.VK_UP: - if (viewport.cursorMode) - { - alignPanel.seqPanel.moveCursor(0,-1); - } - else - moveSelectedSequences(true); - break; + alignPanel.alabels.cancelDrag(); + break; + case KeyEvent.VK_X: + if (evt.isControlDown() || evt.isMetaDown()) + { + cut_actionPerformed(); + } + break; + case KeyEvent.VK_C: + if (viewport.cursorMode && !evt.isControlDown()) + { + alignPanel.seqPanel.setCursorColumn(); + } + if (evt.isControlDown() || evt.isMetaDown()) + { + copy_actionPerformed(); + } + break; + case KeyEvent.VK_V: + if (evt.isControlDown()) + { + paste(evt.isShiftDown()); + } + break; + case KeyEvent.VK_A: + if (evt.isControlDown() || evt.isMetaDown()) + { + selectAllSequenceMenuItem_actionPerformed(); + } + break; + case KeyEvent.VK_DOWN: + if (viewport.cursorMode) + { + alignPanel.seqPanel.moveCursor(0, 1); + } + else + { + moveSelectedSequences(false); + } + break; - case KeyEvent.VK_LEFT: - if(viewport.cursorMode) - { - alignPanel.seqPanel.moveCursor(-1,0); - } - break; + case KeyEvent.VK_UP: + if (viewport.cursorMode) + { + alignPanel.seqPanel.moveCursor(0, -1); + } + else + { + moveSelectedSequences(true); + } + break; - case KeyEvent.VK_RIGHT: - if (viewport.cursorMode) - { - alignPanel.seqPanel.moveCursor(1,0); - } - break; - case KeyEvent.VK_SPACE: - if(viewport.cursorMode) - { - alignPanel.seqPanel.insertGapAtCursor(evt.isControlDown()); - } - break; + case KeyEvent.VK_LEFT: + if (evt.isAltDown() || !viewport.cursorMode) + { + slideSequences(false, alignPanel.seqPanel.getKeyboardNo1()); + } + else + { + alignPanel.seqPanel.moveCursor(-1, 0); + } + break; - case KeyEvent.VK_DELETE: - case KeyEvent.VK_BACK_SPACE: - if(viewport.cursorMode) - { - alignPanel.seqPanel.deleteGapAtCursor(evt.isControlDown()); - } - else - { - cut_actionPerformed(); - alignPanel.seqPanel.seqCanvas.repaint(); - } - break; + case KeyEvent.VK_RIGHT: + if (evt.isAltDown() || !viewport.cursorMode) + { + slideSequences(true, alignPanel.seqPanel.getKeyboardNo1()); + } + else + { + alignPanel.seqPanel.moveCursor(1, 0); + } + break; - case KeyEvent.VK_S: - if(viewport.cursorMode) - { - alignPanel.seqPanel.setCursorRow(); - } - break; - case KeyEvent.VK_P: - if(viewport.cursorMode) - { - alignPanel.seqPanel.setCursorPosition(); - } - break; + case KeyEvent.VK_SPACE: + if (viewport.cursorMode) + { + alignPanel.seqPanel.insertGapAtCursor(evt.isControlDown() + || evt.isShiftDown() || evt.isAltDown()); + } + break; + + case KeyEvent.VK_DELETE: + case KeyEvent.VK_BACK_SPACE: + if (viewport.cursorMode) + { + alignPanel.seqPanel.deleteGapAtCursor(evt.isControlDown() + || evt.isShiftDown() || evt.isAltDown()); + } + else + { + cut_actionPerformed(); + alignPanel.seqPanel.seqCanvas.repaint(); + } + break; + + case KeyEvent.VK_S: + if (viewport.cursorMode) + { + alignPanel.seqPanel.setCursorRow(); + } + break; + case KeyEvent.VK_P: + if (viewport.cursorMode) + { + alignPanel.seqPanel.setCursorPosition(); + } + break; + + case KeyEvent.VK_ENTER: + case KeyEvent.VK_COMMA: + if (viewport.cursorMode) + { + alignPanel.seqPanel.setCursorRowAndColumn(); + } + break; + + case KeyEvent.VK_Q: + if (viewport.cursorMode) + { + alignPanel.seqPanel.setSelectionAreaAtCursor(true); + } + break; + case KeyEvent.VK_M: + if (viewport.cursorMode) + { + alignPanel.seqPanel.setSelectionAreaAtCursor(false); + } + break; + + case KeyEvent.VK_F2: + viewport.cursorMode = !viewport.cursorMode; + statusBar.setText(MessageManager.formatMessage( + "label.keyboard_editing_mode", + new String[] { (viewport.cursorMode ? "on" : "off") })); + if (viewport.cursorMode) + { + alignPanel.seqPanel.seqCanvas.cursorX = ranges.getStartRes(); + alignPanel.seqPanel.seqCanvas.cursorY = ranges.getStartSeq(); + } + break; + + case KeyEvent.VK_F: + if (evt.isControlDown()) + { + findMenuItem_actionPerformed(); + } + break; + + case KeyEvent.VK_H: + { + boolean toggleSeqs = !evt.isControlDown(); + boolean toggleCols = !evt.isShiftDown(); + toggleHiddenRegions(toggleSeqs, toggleCols); + break; + } + + case KeyEvent.VK_PAGE_UP: + if (viewport.getWrapAlignment()) + { + alignPanel.scrollUp(true); + } + else + { + alignPanel.setScrollValues(ranges.getStartRes(), + 2 * ranges.getStartSeq() - ranges.getEndSeq()); + } + break; + + case KeyEvent.VK_PAGE_DOWN: + if (viewport.getWrapAlignment()) + { + alignPanel.scrollUp(false); + } + else + { + alignPanel + .setScrollValues(ranges.getStartRes(), ranges.getEndSeq()); + } + break; - case KeyEvent.VK_ENTER: - case KeyEvent.VK_COMMA: - if(viewport.cursorMode) + case KeyEvent.VK_Z: + if (evt.isControlDown()) + { + undoMenuItem_actionPerformed(); + } + break; + + case KeyEvent.VK_Y: + if (evt.isControlDown()) + { + redoMenuItem_actionPerformed(); + } + break; + + case KeyEvent.VK_L: + if (evt.isControlDown()) + { + trimAlignment(true); + } + break; + + case KeyEvent.VK_R: + if (evt.isControlDown()) + { + trimAlignment(false); + } + break; + + case KeyEvent.VK_E: + if (evt.isControlDown()) + { + if (evt.isShiftDown()) { - alignPanel.seqPanel.setCursorRowAndColumn(); + this.removeAllGapsMenuItem_actionPerformed(); } - break; - - case KeyEvent.VK_Q: - if(viewport.cursorMode) + else { - alignPanel.seqPanel.setSelectionAreaAtCursor(true); + removeGappedColumnMenuItem_actionPerformed(); } - break; - case KeyEvent.VK_M: - if(viewport.cursorMode) + } + break; + case KeyEvent.VK_I: + if (evt.isControlDown()) + { + if (evt.isAltDown()) { - alignPanel.seqPanel.setSelectionAreaAtCursor(false); + invertColSel_actionPerformed(); } - break; - - case KeyEvent.VK_F2: - viewport.cursorMode = ! viewport.cursorMode; - statusBar.setText("Keyboard editing mode is "+ - (viewport.cursorMode ? "on" : "off")); - if(viewport.cursorMode) - { - alignPanel.seqPanel.seqCanvas.cursorX = viewport.startRes; - alignPanel.seqPanel.seqCanvas.cursorY = viewport.startSeq; - } - alignPanel.seqPanel.seqCanvas.repaint(); - break; - - case KeyEvent.VK_F: - if (evt.isControlDown()) + else { - findMenuItem_actionPerformed(); + invertSequenceMenuItem_actionPerformed(); } - break; - case KeyEvent.VK_H: - { - boolean toggleSeqs = !evt.isControlDown(); - boolean toggleCols = !evt.isShiftDown(); - boolean hide = false; - SequenceGroup sg = viewport.getSelectionGroup(); + } + break; - if(toggleSeqs) + case KeyEvent.VK_G: + if (evt.isControlDown()) + { + if (evt.isShiftDown()) { - if (sg != null && sg.getSize(false) != viewport.alignment.getHeight()) - { - hide = true; - viewport.hideAllSelectedSeqs(); - } - else if (!(toggleCols && viewport.colSel.getSelected().size() > 0)) - viewport.showAllHiddenSeqs(); + this.unGroup_actionPerformed(); } - - if(toggleCols) + else { - if (viewport.colSel.getSelected().size() > 0) - { - viewport.hideSelectedColumns(); - if(!toggleSeqs) - viewport.selectionGroup = sg; - } - else if (!hide) - viewport.showAllHiddenColumns(); + this.createGroup_actionPerformed(); } + } + break; - alignPanel.repaint(); - break; + case KeyEvent.VK_U: + if (evt.isControlDown()) + { + this.deleteGroups_actionPerformed(); + } + break; + + case KeyEvent.VK_T: + if (evt.isControlDown()) + { + newView(null); } + break; } + alignPanel.paintAlignment(true); } - public void keyReleased(KeyEvent evt) - {} - public void keyTyped(KeyEvent evt) - {} - -public void itemStateChanged(ItemEvent evt) - { - if(evt.getSource()==colourTextMenuItem) - colourTextMenuItem_actionPerformed(); - else if(evt.getSource()==wrapMenuItem) - wrapMenuItem_actionPerformed(); - else if(evt.getSource()==scaleAbove) - scaleAbove_actionPerformed(); - else if(evt.getSource()==scaleLeft) - scaleLeft_actionPerformed(); - else if(evt.getSource()==scaleRight) - scaleRight_actionPerformed(); - else if(evt.getSource()==seqLimits) - seqLimits_itemStateChanged(); - else if(evt.getSource()==viewBoxesMenuItem) - viewBoxesMenuItem_actionPerformed(); - else if(evt.getSource()==viewTextMenuItem) - viewTextMenuItem_actionPerformed(); - else if(evt.getSource()==renderGapsMenuItem) - renderGapsMenuItem_actionPerformed(); - else if(evt.getSource()==annotationPanelMenuItem) - annotationPanelMenuItem_actionPerformed(); - else if(evt.getSource()==sequenceFeatures) - { - viewport.showSequenceFeatures(sequenceFeatures.getState()); - alignPanel.seqPanel.seqCanvas.repaint(); - } - else if(evt.getSource()==conservationMenuItem) - conservationMenuItem_actionPerformed(); - else if(evt.getSource()==abovePIDThreshold) - abovePIDThreshold_actionPerformed(); - else if(evt.getSource()==applyToAllGroups) - applyToAllGroups_actionPerformed(); - else if(evt.getSource()==autoCalculate) - viewport.autocalculateConsensus = autoCalculate.getState(); - } - public void actionPerformed(ActionEvent evt) - { - Object source = evt.getSource(); - if(source==inputText) - inputText_actionPerformed(); - else if(source==loadTree) - loadTree_actionPerformed(); - else if(source==loadApplication) - launchFullApplication(); - else if(source==closeMenuItem) - closeMenuItem_actionPerformed(); - else if(source==copy) - copy_actionPerformed(); - else if(source==undoMenuItem) - undoMenuItem_actionPerformed(); - else if(source==redoMenuItem) - redoMenuItem_actionPerformed(); - else if(source==inputText) - inputText_actionPerformed(); - else if(source==closeMenuItem) - closeMenuItem_actionPerformed(); - else if(source==undoMenuItem) - undoMenuItem_actionPerformed(); - else if(source==redoMenuItem) - redoMenuItem_actionPerformed(); - else if(source==copy) - copy_actionPerformed(); - else if(source==pasteNew) - pasteNew_actionPerformed(); - else if(source==pasteThis) - pasteThis_actionPerformed(); - else if(source==cut) - cut_actionPerformed(); - else if(source==delete) - delete_actionPerformed(); - else if(source==deleteGroups) - deleteGroups_actionPerformed(); - else if(source==selectAllSequenceMenuItem) - selectAllSequenceMenuItem_actionPerformed(); - else if(source==deselectAllSequenceMenuItem) - deselectAllSequenceMenuItem_actionPerformed(); - else if(source==invertSequenceMenuItem) - invertSequenceMenuItem_actionPerformed(); - else if(source==invertColSel) - { viewport.invertColumnSelection(); alignPanel.repaint(); } - else if(source==remove2LeftMenuItem) - remove2LeftMenuItem_actionPerformed(); - else if(source==remove2RightMenuItem) - remove2RightMenuItem_actionPerformed(); - else if(source==removeGappedColumnMenuItem) - removeGappedColumnMenuItem_actionPerformed(); - else if(source==removeAllGapsMenuItem) - removeAllGapsMenuItem_actionPerformed(); - else if(source==findMenuItem) - findMenuItem_actionPerformed(); - else if(source==font) - font_actionPerformed(); - else if(source==showColumns) - { - viewport.showAllHiddenColumns(); alignPanel.repaint(); - } - else if(source==showSeqs) + /** + * called by key handler and the hide all/show all menu items + * + * @param toggleSeqs + * @param toggleCols + */ + private void toggleHiddenRegions(boolean toggleSeqs, boolean toggleCols) + { + boolean hide = false; + SequenceGroup sg = viewport.getSelectionGroup(); + if (!toggleSeqs && !toggleCols) { - viewport.showAllHiddenSeqs(); + // Hide everything by the current selection - this is a hack - we do the + // invert and then hide + // first check that there will be visible columns after the invert. + if (viewport.hasSelectedColumns() + || (sg != null && sg.getSize() > 0 && sg.getStartRes() <= sg + .getEndRes())) + { + // now invert the sequence set, if required - empty selection implies + // that no hiding is required. + if (sg != null) + { + invertSequenceMenuItem_actionPerformed(); + sg = viewport.getSelectionGroup(); + toggleSeqs = true; + + } + viewport.expandColSelection(sg, true); + // finally invert the column selection and get the new sequence + // selection and indicate it should be hidden. + invertColSel_actionPerformed(); + toggleCols = true; + } + } + + if (toggleSeqs) + { + if (sg != null && sg.getSize() != viewport.getAlignment().getHeight()) + { + hide = true; + viewport.hideAllSelectedSeqs(); + } + else if (!(toggleCols && viewport.hasSelectedColumns())) + { + viewport.showAllHiddenSeqs(); + } + } + + if (toggleCols) + { + if (viewport.hasSelectedColumns()) + { + viewport.hideSelectedColumns(); + if (!toggleSeqs) + { + viewport.setSelectionGroup(sg); + } + } + else if (!hide) + { + viewport.showAllHiddenColumns(); + } + viewport.sendSelection(); + } + } + + @Override + public void keyReleased(KeyEvent evt) + { + } + + @Override + public void keyTyped(KeyEvent evt) + { + } + + @Override + public void itemStateChanged(ItemEvent evt) + { + final Object source = evt.getSource(); + if (source == displayNonconservedMenuItem) + { + displayNonconservedMenuItem_actionPerformed(); + } + else if (source == colourTextMenuItem) + { + colourTextMenuItem_actionPerformed(); + } + else if (source == wrapMenuItem) + { + wrapMenuItem_actionPerformed(); + } + else if (source == scaleAbove) + { + viewport.setScaleAboveWrapped(scaleAbove.getState()); + } + else if (source == scaleLeft) + { + viewport.setScaleLeftWrapped(scaleLeft.getState()); + } + else if (source == scaleRight) + { + viewport.setScaleRightWrapped(scaleRight.getState()); + } + else if (source == seqLimits) + { + seqLimits_itemStateChanged(); + } + else if (source == viewBoxesMenuItem) + { + viewport.setShowBoxes(viewBoxesMenuItem.getState()); + } + else if (source == viewTextMenuItem) + { + viewport.setShowText(viewTextMenuItem.getState()); + } + else if (source == renderGapsMenuItem) + { + viewport.setRenderGaps(renderGapsMenuItem.getState()); + } + else if (source == annotationPanelMenuItem) + { + boolean showAnnotations = annotationPanelMenuItem.getState(); + showAlignmentAnnotations.setEnabled(showAnnotations); + showSequenceAnnotations.setEnabled(showAnnotations); + viewport.setShowAnnotation(showAnnotations); + alignPanel.setAnnotationVisible(showAnnotations); + } + else if (source == sequenceFeatures) + { + viewport.setShowSequenceFeatures(sequenceFeatures.getState()); + alignPanel.seqPanel.seqCanvas.repaint(); + } + else if (source == showAlignmentAnnotations) + { + setAnnotationsVisibility(); + } + else if (source == showSequenceAnnotations) + { + setAnnotationsVisibility(); + } + else if (source == sortAnnBySequence) + { + boolean newState = sortAnnBySequence.getState(); + sortAnnByLabel.setState(false); + setAnnotationSortOrder(newState ? SequenceAnnotationOrder.SEQUENCE_AND_LABEL + : SequenceAnnotationOrder.NONE); + setViewportAnnotationOrder(); + } + else if (source == sortAnnByLabel) + { + boolean newState = sortAnnByLabel.getState(); + sortAnnBySequence.setState(false); + setAnnotationSortOrder(newState ? SequenceAnnotationOrder.LABEL_AND_SEQUENCE + : SequenceAnnotationOrder.NONE); + setViewportAnnotationOrder(); + } + else if (source == showAutoFirst) + { + showAutoLast.setState(!showAutoFirst.getState()); + setShowAutoCalculatedAbove(showAutoFirst.getState()); + setViewportAnnotationOrder(); + } + else if (source == showAutoLast) + { + showAutoFirst.setState(!showAutoLast.getState()); + setShowAutoCalculatedAbove(showAutoFirst.getState()); + setViewportAnnotationOrder(); + } + else if (source == conservationMenuItem) + { + conservationMenuItem_actionPerformed(); + } + else if (source == abovePIDThreshold) + { + abovePIDThreshold_actionPerformed(); + } + else if (source == applyToAllGroups) + { + viewport.setColourAppliesToAllGroups(applyToAllGroups.getState()); + } + else if (source == autoCalculate) + { + viewport.autoCalculateConsensus = autoCalculate.getState(); + } + else if (source == sortByTree) + { + viewport.sortByTree = sortByTree.getState(); + } + else if (source == this.centreColumnLabelFlag) + { + centreColumnLabelFlag_stateChanged(); + } + else if (source == this.followMouseOverFlag) + { + mouseOverFlag_stateChanged(); + } + else if (source == showGroupConsensus) + { + showGroupConsensus_actionPerformed(); + } + else if (source == showGroupConservation) + { + showGroupConservation_actionPerformed(); + } + else if (source == showSequenceLogo) + { + showSequenceLogo_actionPerformed(); + } + else if (source == normSequenceLogo) + { + normSequenceLogo_actionPerformed(); + } + else if (source == showConsensusHistogram) + { + showConsensusHistogram_actionPerformed(); + } + else if (source == applyAutoAnnotationSettings) + { + applyAutoAnnotationSettings_actionPerformed(); + } + alignPanel.paintAlignment(true); + } + + /** + * Set the visibility state of sequence-related and/or alignment-related + * annotations depending on checkbox selections, and repaint. + * + * @param visible + */ + private void setAnnotationsVisibility() + { + boolean showForAlignment = showAlignmentAnnotations.getState(); + boolean showForSequences = showSequenceAnnotations.getState(); + if (alignPanel.getAlignment().getAlignmentAnnotation() != null) + { + for (AlignmentAnnotation aa : alignPanel.getAlignment() + .getAlignmentAnnotation()) + { + boolean visible = (aa.sequenceRef == null ? showForAlignment + : showForSequences); + aa.visible = visible; + } + } + alignPanel.validateAnnotationDimensions(true); + validate(); + repaint(); + } + + private void setAnnotationSortOrder(SequenceAnnotationOrder order) + { + this.annotationSortOrder = order; + } + + /** + * Set flags on the viewport that control annotation ordering + */ + private void setViewportAnnotationOrder() + { + this.alignPanel.av.setSortAnnotationsBy(this.annotationSortOrder); + this.alignPanel.av + .setShowAutocalculatedAbove(this.showAutoCalculatedAbove); + } + + private void setShowAutoCalculatedAbove(boolean showAbove) + { + this.showAutoCalculatedAbove = showAbove; + } + + private void mouseOverFlag_stateChanged() + { + viewport.setFollowHighlight(followMouseOverFlag.getState()); + // TODO: could kick the scrollTo mechanism to reset view for current + // searchresults. + } + + private void centreColumnLabelFlag_stateChanged() + { + viewport.centreColumnLabels = centreColumnLabelFlag.getState(); + this.alignPanel.annotationPanel.repaint(); + } + + @Override + public void actionPerformed(ActionEvent evt) + { + viewport.applet.currentAlignFrame = this; + + Object source = evt.getSource(); + + if (source == inputText) + { + inputText_actionPerformed(); + } + else if (source == loadTree) + { + loadTree_actionPerformed(); + } + else if (source == loadApplication) + { + launchFullApplication(); + } + else if (source == loadAnnotations) + { + loadAnnotations(); + } + else if (source == outputAnnotations) + { + outputAnnotations(true); + } + else if (source == outputFeatures) + { + outputFeatures(true, "Jalview"); + } + else if (source == closeMenuItem) + { + closeMenuItem_actionPerformed(); + } + else if (source == copy) + { + copy_actionPerformed(); + } + else if (source == undoMenuItem) + { + undoMenuItem_actionPerformed(); + } + else if (source == redoMenuItem) + { + redoMenuItem_actionPerformed(); + } + else if (source == inputText) + { + inputText_actionPerformed(); + } + else if (source == closeMenuItem) + { + closeMenuItem_actionPerformed(); + } + else if (source == undoMenuItem) + { + undoMenuItem_actionPerformed(); + } + else if (source == redoMenuItem) + { + redoMenuItem_actionPerformed(); + } + else if (source == copy) + { + copy_actionPerformed(); + } + else if (source == pasteNew) + { + pasteNew_actionPerformed(); + } + else if (source == pasteThis) + { + pasteThis_actionPerformed(); + } + else if (source == cut) + { + cut_actionPerformed(); + } + else if (source == delete) + { + delete_actionPerformed(); + } + else if (source == grpsFromSelection) + { + makeGrpsFromSelection_actionPerformed(); + } + else if (source == deleteGroups) + { + deleteGroups_actionPerformed(); + } + else if (source == selectAllSequenceMenuItem) + { + selectAllSequenceMenuItem_actionPerformed(); + } + else if (source == deselectAllSequenceMenuItem) + { + deselectAllSequenceMenuItem_actionPerformed(); + } + else if (source == invertSequenceMenuItem) + { + invertSequenceMenuItem_actionPerformed(); + // uncomment to slave sequence selections in split frame + // viewport.sendSelection(); + } + else if (source == invertColSel) + { + viewport.invertColumnSelection(); + alignPanel.paintAlignment(true); + viewport.sendSelection(); + } + else if (source == remove2LeftMenuItem) + { + trimAlignment(true); + } + else if (source == remove2RightMenuItem) + { + trimAlignment(false); + } + else if (source == removeGappedColumnMenuItem) + { + removeGappedColumnMenuItem_actionPerformed(); + } + else if (source == removeAllGapsMenuItem) + { + removeAllGapsMenuItem_actionPerformed(); + } + else if (source == findMenuItem) + { + findMenuItem_actionPerformed(); + } + else if (source == font) + { + new FontChooser(alignPanel); + } + else if (source == newView) + { + newView(null); + } + else if (source == showColumns) + { + viewport.showAllHiddenColumns(); + alignPanel.paintAlignment(true); + viewport.sendSelection(); + } + else if (source == showSeqs) + { + viewport.showAllHiddenSeqs(); + alignPanel.paintAlignment(true); + // uncomment if we want to slave sequence selections in split frame + // viewport.sendSelection(); + } + else if (source == hideColumns) + { + viewport.hideSelectedColumns(); + alignPanel.paintAlignment(true); + viewport.sendSelection(); + } + else if (source == hideSequences + && viewport.getSelectionGroup() != null) + { + viewport.hideAllSelectedSeqs(); + alignPanel.paintAlignment(true); + // uncomment if we want to slave sequence selections in split frame + // viewport.sendSelection(); + } + else if (source == hideAllButSelection) + { + toggleHiddenRegions(false, false); + alignPanel.paintAlignment(true); + viewport.sendSelection(); + } + else if (source == hideAllSelection) + { + SequenceGroup sg = viewport.getSelectionGroup(); + viewport.expandColSelection(sg, false); + viewport.hideAllSelectedSeqs(); + viewport.hideSelectedColumns(); + alignPanel.paintAlignment(true); + viewport.sendSelection(); + } + else if (source == showAllHidden) + { + viewport.showAllHiddenColumns(); + viewport.showAllHiddenSeqs(); + alignPanel.paintAlignment(true); + viewport.sendSelection(); + } + else if (source == showGroupConsensus) + { + showGroupConsensus_actionPerformed(); + } + else if (source == showGroupConservation) + { + showGroupConservation_actionPerformed(); + } + else if (source == showSequenceLogo) + { + showSequenceLogo_actionPerformed(); + } + else if (source == normSequenceLogo) + { + normSequenceLogo_actionPerformed(); + } + else if (source == showConsensusHistogram) + { + showConsensusHistogram_actionPerformed(); + } + else if (source == applyAutoAnnotationSettings) + { + applyAutoAnnotationSettings_actionPerformed(); + } + else if (source == featureSettings) + { + new FeatureSettings(alignPanel); + } + else if (source == alProperties) + { + StringBuffer contents = new jalview.io.AlignmentProperties( + viewport.getAlignment()).formatAsString(); + CutAndPasteTransfer cap = new CutAndPasteTransfer(false, this); + cap.setText(contents.toString()); + Frame frame = new Frame(); + frame.add(cap); + jalview.bin.JalviewLite.addFrame(frame, MessageManager.formatMessage( + "label.alignment_properties", new String[] { getTitle() }), + 400, 250); + } + else if (source == overviewMenuItem) + { + overviewMenuItem_actionPerformed(); + } + else if (source == noColourmenuItem) + { + changeColour(null); + } + else if (source == clustalColour) + { + abovePIDThreshold.setState(false); + changeColour(new ClustalxColourScheme(viewport.getAlignment(), null)); + } + else if (source == zappoColour) + { + changeColour(new ZappoColourScheme()); + } + else if (source == taylorColour) + { + changeColour(new TaylorColourScheme()); + } + else if (source == hydrophobicityColour) + { + changeColour(new HydrophobicColourScheme()); + } + else if (source == helixColour) + { + changeColour(new HelixColourScheme()); + } + else if (source == strandColour) + { + changeColour(new StrandColourScheme()); + } + else if (source == turnColour) + { + changeColour(new TurnColourScheme()); + } + else if (source == buriedColour) + { + changeColour(new BuriedColourScheme()); + } + else if (source == nucleotideColour) + { + changeColour(new NucleotideColourScheme()); + } + else if (source == purinePyrimidineColour) + { + changeColour(new PurinePyrimidineColourScheme()); + } + // else if (source == RNAInteractionColour) + // { + // changeColour(new RNAInteractionColourScheme()); + // } + else if (source == RNAHelixColour) + { + changeColour(new RNAHelicesColour(viewport.getAlignment())); + // new RNAHelicesColourChooser(viewport, alignPanel); + } + else if (source == modifyPID) + { + modifyPID_actionPerformed(); + } + else if (source == modifyConservation) + { + modifyConservation_actionPerformed(); + } + else if (source == userDefinedColour) + { + new UserDefinedColours(alignPanel, null); + } + else if (source == PIDColour) + { + changeColour(new PIDColourScheme()); + } + else if (source == BLOSUM62Colour) + { + changeColour(new Blosum62ColourScheme()); + } + else if (source == tcoffeeColour) + { + changeColour(new TCoffeeColourScheme(alignPanel.getAlignment())); + } + else if (source == annotationColour) + { + new AnnotationColourChooser(viewport, alignPanel); + } + else if (source == annotationColumnSelection) + { + new AnnotationColumnChooser(viewport, alignPanel); + } + else if (source == sortPairwiseMenuItem) + { + sortPairwiseMenuItem_actionPerformed(); + } + else if (source == sortIDMenuItem) + { + sortIDMenuItem_actionPerformed(); + } + else if (source == sortLengthMenuItem) + { + sortLengthMenuItem_actionPerformed(); + } + else if (source == sortGroupMenuItem) + { + sortGroupMenuItem_actionPerformed(); + } + else if (source == removeRedundancyMenuItem) + { + removeRedundancyMenuItem_actionPerformed(); + } + else if (source == pairwiseAlignmentMenuItem) + { + pairwiseAlignmentMenuItem_actionPerformed(); + } + else if (source == PCAMenuItem) + { + PCAMenuItem_actionPerformed(); + } + else if (source == averageDistanceTreeMenuItem) + { + averageDistanceTreeMenuItem_actionPerformed(); + } + else if (source == neighbourTreeMenuItem) + { + neighbourTreeMenuItem_actionPerformed(); + } + else if (source == njTreeBlosumMenuItem) + { + njTreeBlosumMenuItem_actionPerformed(); + } + else if (source == avDistanceTreeBlosumMenuItem) + { + avTreeBlosumMenuItem_actionPerformed(); + } + else if (source == documentation) + { + documentation_actionPerformed(); + } + else if (source == about) + { + about_actionPerformed(); + } + + } + + public void inputText_actionPerformed() + { + CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this); + Frame frame = new Frame(); + frame.add(cap); + jalview.bin.JalviewLite.addFrame(frame, + MessageManager.getString("label.input_cut_paste"), 500, 500); + } + + protected void outputText_actionPerformed(ActionEvent e) + { + CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this); + Frame frame = new Frame(); + frame.add(cap); + JalviewLite.addFrame(frame, MessageManager.formatMessage( + "label.alignment_output_command", + new Object[] { e.getActionCommand() }), 600, 500); + + FileFormatI fileFormat = FileFormats.getInstance().forName( + e.getActionCommand()); + cap.setText(new AppletFormatAdapter(alignPanel).formatSequences( + fileFormat, viewport.getAlignment(), + viewport.getShowJVSuffix())); + } + + public void loadAnnotations() + { + CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this); + cap.setText(MessageManager + .getString("label.paste_features_annotations_Tcoffee_here")); + cap.setAnnotationImport(); + Frame frame = new Frame(); + frame.add(cap); + jalview.bin.JalviewLite.addFrame(frame, + MessageManager.getString("action.paste_annotations"), 400, 300); + + } + + public String outputAnnotations(boolean displayTextbox) + { + String annotation = new AnnotationFile() + .printAnnotationsForView(viewport); + + if (displayTextbox) + { + CutAndPasteTransfer cap = new CutAndPasteTransfer(false, this); + Frame frame = new Frame(); + frame.add(cap); + jalview.bin.JalviewLite.addFrame(frame, + MessageManager.getString("label.annotations"), 600, 500); + cap.setText(annotation); + } + + return annotation; + } + + private Map getDisplayedFeatureCols() + { + if (alignPanel.getFeatureRenderer() != null + && viewport.getFeaturesDisplayed() != null) + { + return alignPanel.getFeatureRenderer().getDisplayedFeatureCols(); + + } + return null; + } + + public String outputFeatures(boolean displayTextbox, String format) + { + String features; + FeaturesFile formatter = new FeaturesFile(); + if (format.equalsIgnoreCase("Jalview")) + { + features = formatter.printJalviewFormat(viewport.getAlignment() + .getSequencesArray(), getDisplayedFeatureCols()); + } + else + { + features = formatter.printGffFormat(viewport.getAlignment() + .getSequencesArray(), getDisplayedFeatureCols()); + } + + if (displayTextbox) + { + boolean frimport = false; + if (features == null || features.equals("No Features Visible")) + { + features = "# No features visible - paste some and import them here."; + frimport = true; + } + + CutAndPasteTransfer cap = new CutAndPasteTransfer(frimport, this); + if (frimport) + { + cap.setAnnotationImport(); + } + Frame frame = new Frame(); + frame.add(cap); + jalview.bin.JalviewLite.addFrame(frame, + MessageManager.getString("label.features"), 600, 500); + cap.setText(features); + } + else + { + if (features == null) + { + features = ""; + } + } + + return features; + } + + void launchFullApplication() + { + StringBuffer url = new StringBuffer(jalviewServletURL); + + // allow servlet parameters to be passed in applet parameter + String firstSep = url.lastIndexOf("?") > url.lastIndexOf("/") ? "&" + : "?"; + url.append(firstSep); + + url.append("open=" + + appendProtocol(viewport.applet.getParameter("file"))); + + if (viewport.applet.getParameter("features") != null) + { + url.append("&features="); + url.append(appendProtocol(viewport.applet.getParameter("features"))); + } + + if (viewport.applet.getParameter("annotations") != null) + { + url.append("&annotations="); + url.append(appendProtocol(viewport.applet.getParameter("annotations"))); + } + + if (viewport.applet.getParameter("jnetfile") != null + || viewport.applet.getParameter("jpredfile") != null) + { + url.append("&annotations="); + url.append(appendProtocol(viewport.applet.getParameter("jnetfile") != null ? viewport.applet + .getParameter("jnetfile") : viewport.applet + .getParameter("jpredfile"))); + } + + if (viewport.applet.getParameter("defaultColour") != null) + { + url.append("&colour=" + + removeWhiteSpace(viewport.applet + .getParameter("defaultColour"))); + } + + if (viewport.applet.getParameter("userDefinedColour") != null) + { + url.append("&colour=" + + removeWhiteSpace(viewport.applet + .getParameter("userDefinedColour"))); + } + if (viewport.applet.getParameter("tree") != null) + { + url.append("&tree=" + + appendProtocol(viewport.applet.getParameter("tree"))); + } + if (viewport.applet.getParameter("treeFile") != null) + { + url.append("&tree=" + + appendProtocol(viewport.applet.getParameter("treeFile"))); + } + + showURL(url.toString(), "FULL_APP"); + } + + String removeWhiteSpace(String colour) + { + StringBuffer sb = new StringBuffer(); + for (int i = 0; i < colour.length(); i++) + { + if (Character.isWhitespace(colour.charAt(i))) + { + sb.append("%20"); + } + else + { + sb.append(colour.charAt(i)); + } + } + + return sb.toString(); + } + + String appendProtocol(String url) + { + try + { + new URL(url); + url = URLEncoder.encode(url); + } + /* + * When we finally deprecate 1.1 compatibility, we can start to use + * URLEncoder.encode(url,"UTF-8") and then we'll need this catch: catch + * (UnsupportedEncodingException ex) { System.err.println("WARNING - + * IMPLEMENTATION ERROR - UNSUPPORTED ENCODING EXCEPTION FOR "+url); + * ex.printStackTrace(); } + */ + catch (java.net.MalformedURLException ex) + { + url = viewport.applet.getCodeBase() + url; + } + return url; + } + + public void closeMenuItem_actionPerformed() + { + PaintRefresher.RemoveComponent(alignPanel); + if (alignPanel.seqPanel != null + && alignPanel.seqPanel.seqCanvas != null) + { + PaintRefresher.RemoveComponent(alignPanel.seqPanel.seqCanvas); + } + if (alignPanel.idPanel != null && alignPanel.idPanel.idCanvas != null) + { + PaintRefresher.RemoveComponent(alignPanel.idPanel.idCanvas); + } + + if (PaintRefresher.components.size() == 0 && viewport.applet == null) + { + System.exit(0); + } + else + { + } + viewport = null; + alignPanel = null; + this.dispose(); + } + + /** + * TODO: JAL-1104 + */ + void updateEditMenuBar() + { + + if (viewport.getHistoryList().size() > 0) + { + undoMenuItem.setEnabled(true); + CommandI command = viewport.getHistoryList().peek(); + undoMenuItem.setLabel(MessageManager.formatMessage( + "label.undo_command", + new Object[] { command.getDescription() })); + } + else + { + undoMenuItem.setEnabled(false); + undoMenuItem.setLabel(MessageManager.getString("action.undo")); + } + + if (viewport.getRedoList().size() > 0) + { + redoMenuItem.setEnabled(true); + + CommandI command = viewport.getRedoList().peek(); + redoMenuItem.setLabel(MessageManager.formatMessage( + "label.redo_command", + new Object[] { command.getDescription() })); + } + else + { + redoMenuItem.setEnabled(false); + redoMenuItem.setLabel(MessageManager.getString("action.redo")); + } + } + + /** + * TODO: JAL-1104 + */ + @Override + public void addHistoryItem(CommandI command) + { + if (command.getSize() > 0) + { + viewport.addToHistoryList(command); + viewport.clearRedoList(); + updateEditMenuBar(); + viewport.updateHiddenColumns(); + } + } + + /** + * TODO: JAL-1104 DOCUMENT ME! + * + * @param e + * DOCUMENT ME! + */ + protected void undoMenuItem_actionPerformed() + { + if (viewport.getHistoryList().isEmpty()) + { + return; + } + + CommandI command = viewport.getHistoryList().pop(); + viewport.addToRedoList(command); + command.undoCommand(null); + + AlignmentViewport originalSource = getOriginatingSource(command); + // JBPNote Test + if (originalSource != viewport) + { + System.err + .println("Warning: Viewport object mismatch whilst undoing"); + } + originalSource.updateHiddenColumns(); // originalSource.hasHiddenColumns = + // viewport.getColumnSelection().getHiddenColumns() + // != null; + updateEditMenuBar(); + originalSource.firePropertyChange("alignment", null, originalSource + .getAlignment().getSequences()); + } + + /** + * TODO: JAL-1104 DOCUMENT ME! + * + * @param e + * DOCUMENT ME! + */ + protected void redoMenuItem_actionPerformed() + { + if (viewport.getRedoList().isEmpty()) + { + return; + } + + CommandI command = viewport.getRedoList().pop(); + viewport.addToHistoryList(command); + command.doCommand(null); + + AlignmentViewport originalSource = getOriginatingSource(command); + // JBPNote Test + if (originalSource != viewport) + { + System.err + .println("Warning: Viewport object mismatch whilst re-doing"); + } + originalSource.updateHiddenColumns(); // sethasHiddenColumns(); = + // viewport.getColumnSelection().getHiddenColumns() + // != null; + + updateEditMenuBar(); + originalSource.firePropertyChange("alignment", null, originalSource + .getAlignment().getSequences()); + } + + AlignmentViewport getOriginatingSource(CommandI command) + { + AlignmentViewport originalSource = null; + // For sequence removal and addition, we need to fire + // the property change event FROM the viewport where the + // original alignment was altered + AlignmentI al = null; + if (command instanceof EditCommand) + { + EditCommand editCommand = (EditCommand) command; + al = editCommand.getAlignment(); + 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.getAlignment()) + { + originalSource = ((AlignmentPanel) comps.elementAt(i)).av; + break; + } + } + } + } + + if (originalSource == null) + { + // The original view is closed, we must validate + // the current view against the closed view first + if (al != null) + { + PaintRefresher.validateSequences(al, viewport.getAlignment()); + } + + originalSource = viewport; + } + + return originalSource; + } + + /** + * Move the currently selected sequences up or down one position in the + * alignment + * + * @param up + */ + public void moveSelectedSequences(boolean up) + { + SequenceGroup sg = viewport.getSelectionGroup(); + if (sg == null) + { + return; + } + viewport.getAlignment().moveSelectedSequencesByOne(sg, + up ? null : viewport.getHiddenRepSequences(), up); + alignPanel.paintAlignment(true); + + /* + * Also move cDNA/protein complement sequences + */ + AlignViewportI complement = viewport.getCodingComplement(); + if (complement != null) + { + SequenceGroup mappedSelection = MappingUtils.mapSequenceGroup(sg, + viewport, complement); + complement.getAlignment().moveSelectedSequencesByOne(mappedSelection, + up ? null : complement.getHiddenRepSequences(), up); + getSplitFrame().getComplement(this).alignPanel.paintAlignment(true); + } + } + + synchronized void slideSequences(boolean right, int size) + { + List sg = new Vector(); + if (viewport.cursorMode) + { + sg.add(viewport.getAlignment().getSequenceAt( + alignPanel.seqPanel.seqCanvas.cursorY)); + } + else if (viewport.getSelectionGroup() != null + && viewport.getSelectionGroup().getSize() != viewport + .getAlignment().getHeight()) + { + sg = viewport.getSelectionGroup().getSequences( + viewport.getHiddenRepSequences()); + } + + if (sg.size() < 1) + { + return; + } + + Vector invertGroup = new Vector(); + + for (int i = 0; i < viewport.getAlignment().getHeight(); i++) + { + if (!sg.contains(viewport.getAlignment().getSequenceAt(i))) + { + invertGroup.addElement(viewport.getAlignment().getSequenceAt(i)); + } + } + + SequenceI[] seqs1 = sg.toArray(new SequenceI[sg.size()]); + + SequenceI[] seqs2 = invertGroup.toArray(new SequenceI[invertGroup + .size()]); + for (int i = 0; i < invertGroup.size(); i++) + { + seqs2[i] = invertGroup.elementAt(i); + } + + SlideSequencesCommand ssc; + if (right) + { + ssc = new SlideSequencesCommand("Slide Sequences", seqs2, seqs1, + size, viewport.getGapCharacter()); + } + else + { + ssc = new SlideSequencesCommand("Slide Sequences", seqs1, seqs2, + size, viewport.getGapCharacter()); + } + + int groupAdjustment = 0; + if (ssc.getGapsInsertedBegin() && right) + { + if (viewport.cursorMode) + { + alignPanel.seqPanel.moveCursor(size, 0); + } + else + { + groupAdjustment = size; + } + } + else if (!ssc.getGapsInsertedBegin() && !right) + { + if (viewport.cursorMode) + { + alignPanel.seqPanel.moveCursor(-size, 0); + } + else + { + groupAdjustment = -size; + } + } + + if (groupAdjustment != 0) + { + viewport.getSelectionGroup().setStartRes( + viewport.getSelectionGroup().getStartRes() + groupAdjustment); + viewport.getSelectionGroup().setEndRes( + viewport.getSelectionGroup().getEndRes() + groupAdjustment); + } + + boolean appendHistoryItem = false; + Deque historyList = viewport.getHistoryList(); + if (historyList != null && historyList.size() > 0 + && historyList.peek() instanceof SlideSequencesCommand) + { + appendHistoryItem = ssc + .appendSlideCommand((SlideSequencesCommand) historyList + .peek()); + } + + if (!appendHistoryItem) + { + addHistoryItem(ssc); + } + + repaint(); + } + + static StringBuffer copiedSequences; + + static Vector copiedHiddenColumns; + + protected void copy_actionPerformed() + { + if (viewport.getSelectionGroup() == null) + { + return; + } + + SequenceGroup sg = viewport.getSelectionGroup(); + copiedSequences = new StringBuffer(); + Map orderedSeqs = new HashMap(); + for (int i = 0; i < sg.getSize(); i++) + { + SequenceI seq = sg.getSequenceAt(i); + int index = viewport.getAlignment().findIndex(seq); + orderedSeqs.put(index, seq); + } + + int index = 0, startRes, endRes; + char ch; + + if (viewport.hasHiddenColumns() && viewport.getSelectionGroup() != null) + { + copiedHiddenColumns = new Vector(); + int hiddenOffset = viewport.getSelectionGroup().getStartRes(); + for (int[] region : viewport.getColumnSelection().getHiddenColumns()) + { + copiedHiddenColumns.addElement(new int[] { + region[0] - hiddenOffset, region[1] - hiddenOffset }); + } + } + else + { + copiedHiddenColumns = null; + } + + for (int i = 0; i < sg.getSize(); i++) + { + SequenceI seq = null; + + while (seq == null) + { + if (orderedSeqs.containsKey(index)) + { + seq = orderedSeqs.get(index); + index++; + break; + } + else + { + index++; + } + } + + // FIND START RES + // Returns residue following index if gap + startRes = seq.findPosition(sg.getStartRes()); + + // FIND END RES + // Need to find the residue preceeding index if gap + endRes = 0; + + for (int j = 0; j < sg.getEndRes() + 1 && j < seq.getLength(); j++) + { + ch = seq.getCharAt(j); + if (!jalview.util.Comparison.isGap((ch))) + { + endRes++; + } + } + + if (endRes > 0) + { + endRes += seq.getStart() - 1; + } + + copiedSequences.append(seq.getName() + + "\t" + + startRes + + "\t" + + endRes + + "\t" + + seq.getSequenceAsString(sg.getStartRes(), + sg.getEndRes() + 1) + "\n"); + } + + } + + protected void pasteNew_actionPerformed() + { + paste(true); + } + + protected void pasteThis_actionPerformed() + { + paste(false); + } + + void paste(boolean newAlignment) + { + try + { + + if (copiedSequences == null) + { + return; + } + + StringTokenizer st = new StringTokenizer(copiedSequences.toString()); + Vector seqs = new Vector(); + while (st.hasMoreElements()) + { + String name = st.nextToken(); + int start = Integer.parseInt(st.nextToken()); + int end = Integer.parseInt(st.nextToken()); + seqs.addElement(new Sequence(name, st.nextToken(), start, end)); + } + SequenceI[] newSeqs = new SequenceI[seqs.size()]; + for (int i = 0; i < seqs.size(); i++) + { + newSeqs[i] = (SequenceI) seqs.elementAt(i); + } + + if (newAlignment) + { + String newtitle = MessageManager + .getString("label.copied_sequences"); + if (getTitle().startsWith( + MessageManager.getString("label.copied_sequences"))) + { + newtitle = getTitle(); + } + else + { + newtitle = newtitle.concat(MessageManager.formatMessage( + "label.from_msname", new String[] { getTitle() })); + } + AlignFrame af = new AlignFrame(new Alignment(newSeqs), + viewport.applet, newtitle, false); + if (copiedHiddenColumns != null) + { + for (int i = 0; i < copiedHiddenColumns.size(); i++) + { + int[] region = (int[]) copiedHiddenColumns.elementAt(i); + af.viewport.hideColumns(region[0], region[1]); + } + } + + jalview.bin.JalviewLite.addFrame(af, newtitle, frameWidth, + frameHeight); + } + else + { + addSequences(newSeqs); + } + + } catch (Exception ex) + { + } // could be anything being pasted in here + + } + + void addSequences(SequenceI[] seqs) + { + for (int i = 0; i < seqs.length; i++) + { + viewport.getAlignment().addSequence(seqs[i]); + } + + // !newAlignment + addHistoryItem(new EditCommand( + MessageManager.getString("label.add_sequences"), Action.PASTE, + seqs, 0, viewport.getAlignment().getWidth(), + viewport.getAlignment())); + + viewport.getRanges().setEndSeq(viewport.getAlignment().getHeight()); + viewport.getAlignment().getWidth(); + viewport.firePropertyChange("alignment", null, viewport.getAlignment() + .getSequences()); + + } + + protected void cut_actionPerformed() + { + copy_actionPerformed(); + delete_actionPerformed(); + } + + protected void delete_actionPerformed() + { + + SequenceGroup sg = viewport.getSelectionGroup(); + if (sg == null) + { + return; + } + + Vector seqs = new Vector(); + SequenceI seq; + for (int i = 0; i < sg.getSize(); i++) + { + seq = sg.getSequenceAt(i); + seqs.addElement(seq); + } + + /* + * If the cut affects all sequences, warn, remove highlighted columns + */ + if (sg.getSize() == viewport.getAlignment().getHeight()) + { + boolean isEntireAlignWidth = (((sg.getEndRes() - sg.getStartRes()) + 1) == viewport + .getAlignment().getWidth()) ? true : false; + if (isEntireAlignWidth) + { + String title = MessageManager.getString("label.delete_all"); + Panel infoPanel = new Panel(); + infoPanel.setLayout(new FlowLayout()); + infoPanel + .add(new Label(MessageManager.getString("warn.delete_all"))); + + final JVDialog dialog = new JVDialog(this, title, true, 400, 200); + dialog.setMainPanel(infoPanel); + dialog.ok.setLabel(MessageManager.getString("action.ok")); + dialog.cancel.setLabel(MessageManager.getString("action.cancel")); + dialog.setVisible(true); + + if (!dialog.accept) + { + return; + } + } + viewport.getColumnSelection().removeElements(sg.getStartRes(), + sg.getEndRes() + 1); + } + + SequenceI[] cut = new SequenceI[seqs.size()]; + for (int i = 0; i < seqs.size(); i++) + { + cut[i] = (SequenceI) seqs.elementAt(i); + } + + /* + * //ADD HISTORY ITEM + */ + addHistoryItem(new EditCommand( + MessageManager.getString("label.cut_sequences"), Action.CUT, + cut, sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1, + viewport.getAlignment())); + + viewport.setSelectionGroup(null); + viewport.getAlignment().deleteGroup(sg); + + viewport.firePropertyChange("alignment", null, viewport.getAlignment() + .getSequences()); + + if (viewport.getAlignment().getHeight() < 1) + { + this.setVisible(false); + } + viewport.sendSelection(); + } + + /** + * group consensus toggled + * + */ + protected void showGroupConsensus_actionPerformed() + { + viewport.setShowGroupConsensus(showGroupConsensus.getState()); + alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState()); + + } + + /** + * group conservation toggled. + */ + protected void showGroupConservation_actionPerformed() + { + viewport.setShowGroupConservation(showGroupConservation.getState()); + alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState()); + } + + /* + * (non-Javadoc) + * + * @see + * jalview.jbgui.GAlignFrame#showConsensusHistogram_actionPerformed(java.awt + * .event.ActionEvent) + */ + protected void showConsensusHistogram_actionPerformed() + { + viewport.setShowConsensusHistogram(showConsensusHistogram.getState()); + alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState()); + } + + /* + * (non-Javadoc) + * + * @see + * jalview.jbgui.GAlignFrame#showConsensusProfile_actionPerformed(java.awt + * .event.ActionEvent) + */ + protected void showSequenceLogo_actionPerformed() + { + viewport.setShowSequenceLogo(showSequenceLogo.getState()); + alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState()); + } + + protected void normSequenceLogo_actionPerformed() + { + showSequenceLogo.setState(true); + viewport.setShowSequenceLogo(true); + viewport.setNormaliseSequenceLogo(normSequenceLogo.getState()); + alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState()); + } + + protected void applyAutoAnnotationSettings_actionPerformed() + { + alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState()); + } + + protected void makeGrpsFromSelection_actionPerformed() + { + if (avc.makeGroupsFromSelection()) + { + PaintRefresher.Refresh(this, viewport.getSequenceSetId()); + alignPanel.updateAnnotation(); + alignPanel.paintAlignment(true); + } + } + + protected void createGroup_actionPerformed() + { + avc.createGroup(); + } + + protected void unGroup_actionPerformed() + { + if (avc.unGroup()) + { + alignPanel.alignmentChanged(); } - else if(source == hideColumns) + } + + protected void deleteGroups_actionPerformed() + { + if (avc.deleteGroups()) { - viewport.hideSelectedColumns(); alignPanel.repaint(); + alignPanel.alignmentChanged(); } - else if(source == hideSequences && viewport.getSelectionGroup()!=null) + } + + public void selectAllSequenceMenuItem_actionPerformed() + { + SequenceGroup sg = new SequenceGroup(); + for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++) { - viewport.hideAllSelectedSeqs(); + sg.addSequence(viewport.getAlignment().getSequenceAt(i), false); } - else if(source==featureSettings) - featureSettings_actionPerformed(); - else if(source==overviewMenuItem) - overviewMenuItem_actionPerformed(); - else if(source==noColourmenuItem) - noColourmenuItem_actionPerformed(); - else if(source==clustalColour) - clustalColour_actionPerformed(); - else if(source==zappoColour) - zappoColour_actionPerformed(); - else if(source==taylorColour) - taylorColour_actionPerformed(); - else if(source==hydrophobicityColour) - hydrophobicityColour_actionPerformed(); - else if(source==helixColour) - helixColour_actionPerformed(); - else if(source==strandColour) - strandColour_actionPerformed(); - else if(source==turnColour) - turnColour_actionPerformed(); - else if(source==buriedColour) - buriedColour_actionPerformed(); - else if(source==nucleotideColour) - nucleotideColour_actionPerformed(); - else if(source==modifyPID) - modifyPID_actionPerformed(); - else if(source==modifyConservation) - modifyConservation_actionPerformed(); - else if(source==userDefinedColour) - userDefinedColour_actionPerformed(); - else if(source==PIDColour) - PIDColour_actionPerformed(); - else if(source==BLOSUM62Colour) - BLOSUM62Colour_actionPerformed(); - else if(source==annotationColour) - new AnnotationColourChooser(viewport, alignPanel); - else if(source==sortPairwiseMenuItem) - sortPairwiseMenuItem_actionPerformed(); - else if(source==sortIDMenuItem) - sortIDMenuItem_actionPerformed(); - else if(source==sortGroupMenuItem) - sortGroupMenuItem_actionPerformed(); - else if(source==removeRedundancyMenuItem) - removeRedundancyMenuItem_actionPerformed(); - else if(source==pairwiseAlignmentMenuItem) - pairwiseAlignmentMenuItem_actionPerformed(); - else if(source==PCAMenuItem) - PCAMenuItem_actionPerformed(); - else if(source==averageDistanceTreeMenuItem) - averageDistanceTreeMenuItem_actionPerformed(); - else if(source==neighbourTreeMenuItem) - neighbourTreeMenuItem_actionPerformed(); - else if(source==njTreeBlosumMenuItem) - njTreeBlosumMenuItem_actionPerformed(); - else if(source==avDistanceTreeBlosumMenuItem) - avTreeBlosumMenuItem_actionPerformed(); - else if(source==documentation) - documentation_actionPerformed(); - else if(source==about) - about_actionPerformed(); - - } + sg.setEndRes(viewport.getAlignment().getWidth() - 1); + viewport.setSelectionGroup(sg); + // JAL-2034 - should delegate to + // alignPanel to decide if overview needs + // updating. + alignPanel.paintAlignment(false); + PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId()); + viewport.sendSelection(); + } - public void inputText_actionPerformed() + public void deselectAllSequenceMenuItem_actionPerformed() { - CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this); - Frame frame = new Frame(); - frame.add(cap); - jalview.bin.JalviewLite.addFrame(frame, "Cut & Paste Input", 500, 500); + if (viewport.cursorMode) + { + alignPanel.seqPanel.keyboardNo1 = null; + alignPanel.seqPanel.keyboardNo2 = null; + } + viewport.setSelectionGroup(null); + viewport.getColumnSelection().clear(); + viewport.setSelectionGroup(null); + alignPanel.idPanel.idCanvas.searchResults = null; + alignPanel.seqPanel.seqCanvas.highlightSearchResults(null); + // JAL-2034 - should delegate to + // alignPanel to decide if overview needs + // updating. + alignPanel.paintAlignment(false); + PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId()); + viewport.sendSelection(); } - protected void outputText_actionPerformed(ActionEvent e) + public void invertSequenceMenuItem_actionPerformed() { - CutAndPasteTransfer cap = new CutAndPasteTransfer(false, this); - Frame frame = new Frame(); - frame.add(cap); - jalview.bin.JalviewLite.addFrame(frame, - "Alignment output - " + e.getActionCommand(), - 600, 500); - cap.setText(new AppletFormatAdapter().formatSequences(e.getActionCommand(), - viewport.getAlignment().getSequences(), - viewport.showJVSuffix)); + SequenceGroup sg = viewport.getSelectionGroup(); + for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++) + { + sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false); + } + + PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId()); + viewport.sendSelection(); } - void launchFullApplication() + public void invertColSel_actionPerformed() { - StringBuffer url = new StringBuffer(jalviewServletURL); + viewport.invertColumnSelection(); + alignPanel.paintAlignment(true); + PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId()); + viewport.sendSelection(); + } + + void trimAlignment(boolean trimLeft) + { + AlignmentI al = viewport.getAlignment(); + ViewportRanges ranges = viewport.getRanges(); + ColumnSelection colSel = viewport.getColumnSelection(); + int column; + + if (!colSel.isEmpty()) + { + if (trimLeft) + { + column = colSel.getMin(); + } + else + { + column = colSel.getMax(); + } + + SequenceI[] seqs; + if (viewport.getSelectionGroup() != null) + { + seqs = viewport.getSelectionGroup().getSequencesAsArray( + viewport.getHiddenRepSequences()); + } + else + { + seqs = al.getSequencesArray(); + } + + TrimRegionCommand trimRegion; + if (trimLeft) + { + trimRegion = new TrimRegionCommand("Remove Left", true, seqs, + column, al); + ranges.setStartRes(0); + } + else + { + trimRegion = new TrimRegionCommand("Remove Right", false, seqs, + column, al); + } + + statusBar.setText(MessageManager.formatMessage( + "label.removed_columns", + new String[] { Integer.valueOf(trimRegion.getSize()) + .toString() })); + addHistoryItem(trimRegion); + + for (SequenceGroup sg : al.getGroups()) + { + if ((trimLeft && !sg.adjustForRemoveLeft(column)) + || (!trimLeft && !sg.adjustForRemoveRight(column))) + { + al.deleteGroup(sg); + } + } + + viewport.firePropertyChange("alignment", null, al.getSequences()); + } + } + + public void removeGappedColumnMenuItem_actionPerformed() + { + AlignmentI al = viewport.getAlignment(); + ViewportRanges ranges = viewport.getRanges(); + int start = 0; + int end = ranges.getAbsoluteAlignmentWidth() - 1; - url.append("?open="+ - appendProtocol( viewport.applet.getParameter("file") ) ); + SequenceI[] seqs; + if (viewport.getSelectionGroup() != null) + { + seqs = viewport.getSelectionGroup().getSequencesAsArray( + viewport.getHiddenRepSequences()); + start = viewport.getSelectionGroup().getStartRes(); + end = viewport.getSelectionGroup().getEndRes(); + } + else + { + seqs = viewport.getAlignment().getSequencesArray(); + } + + RemoveGapColCommand removeGapCols = new RemoveGapColCommand( + "Remove Gapped Columns", seqs, start, end, + viewport.getAlignment()); + + addHistoryItem(removeGapCols); + + statusBar.setText(MessageManager.formatMessage( + "label.removed_empty_columns", + new String[] { Integer.valueOf(removeGapCols.getSize()) + .toString() })); + + // This is to maintain viewport position on first residue + // of first sequence + SequenceI seq = al.getSequenceAt(0); + int startRes = seq.findPosition(ranges.getStartRes()); + // ShiftList shifts; + // viewport.getAlignment().removeGaps(shifts=new ShiftList()); + // edit.alColumnChanges=shifts.getInverse(); + // if (viewport.hasHiddenColumns) + // viewport.getColumnSelection().compensateForEdits(shifts); + ranges.setStartRes(seq.findIndex(startRes) - 1); + viewport.firePropertyChange("alignment", null, al.getSequences()); + + } + + public void removeAllGapsMenuItem_actionPerformed() + { + AlignmentI al = viewport.getAlignment(); + ViewportRanges ranges = viewport.getRanges(); + int start = 0; + int end = ranges.getAbsoluteAlignmentWidth() - 1; - if(viewport.applet.getParameter("features")!=null) + SequenceI[] seqs; + if (viewport.getSelectionGroup() != null) + { + seqs = viewport.getSelectionGroup().getSequencesAsArray( + viewport.getHiddenRepSequences()); + start = viewport.getSelectionGroup().getStartRes(); + end = viewport.getSelectionGroup().getEndRes(); + } + else { - url.append( "&features=" ); - url.append( appendProtocol( viewport.applet.getParameter("features") ) ); + seqs = viewport.getAlignment().getSequencesArray(); } - if(viewport.applet.getParameter("annotations")!=null) + // This is to maintain viewport position on first residue + // of first sequence + SequenceI seq = al.getSequenceAt(0); + int startRes = seq.findPosition(ranges.getStartRes()); + + addHistoryItem(new RemoveGapsCommand("Remove Gaps", seqs, start, end, + al)); + + ranges.setStartRes(seq.findIndex(startRes) - 1); + + viewport.firePropertyChange("alignment", null, al.getSequences()); + + } + + public void findMenuItem_actionPerformed() + { + new Finder(alignPanel); + } + + /** + * create a new view derived from the current view + * + * @param viewtitle + * @return frame for the new view + */ + public AlignFrame newView(String viewtitle) + { + AlignmentI newal; + if (viewport.hasHiddenRows()) + { + newal = new Alignment(viewport.getAlignment().getHiddenSequences() + .getFullAlignment().getSequencesArray()); + } + else { - url.append( "&annotations=" ); - url.append( appendProtocol( viewport.applet.getParameter("annotations") ) ); + newal = new Alignment(viewport.getAlignment().getSequencesArray()); } - if(viewport.applet.getParameter("defaultColour")!=null) + if (viewport.getAlignment().getAlignmentAnnotation() != null) { - url.append("&colour=" + - removeWhiteSpace(viewport.applet.getParameter("defaultColour")) - ); + for (int i = 0; i < viewport.getAlignment().getAlignmentAnnotation().length; i++) + { + if (!viewport.getAlignment().getAlignmentAnnotation()[i].autoCalculated) + { + newal.addAnnotation(viewport.getAlignment() + .getAlignmentAnnotation()[i]); + } + } } - if(viewport.applet.getParameter("userDefinedColour")!=null) + AlignFrame newaf = new AlignFrame(newal, viewport.applet, "", false); + + newaf.viewport.setSequenceSetId(alignPanel.av.getSequenceSetId()); + PaintRefresher.Register(alignPanel, alignPanel.av.getSequenceSetId()); + PaintRefresher.Register(newaf.alignPanel, + newaf.alignPanel.av.getSequenceSetId()); + + PaintRefresher.Register(newaf.alignPanel.idPanel.idCanvas, + newaf.alignPanel.av.getSequenceSetId()); + PaintRefresher.Register(newaf.alignPanel.seqPanel.seqCanvas, + newaf.alignPanel.av.getSequenceSetId()); + + Vector comps = (Vector) PaintRefresher.components.get(viewport + .getSequenceSetId()); + int viewSize = -1; + for (int i = 0; i < comps.size(); i++) { - url.append( "&colour=" + - removeWhiteSpace( viewport.applet.getParameter("userDefinedColour") ) - ); + if (comps.elementAt(i) instanceof AlignmentPanel) + { + viewSize++; + } } - showURL(url.toString(), "FULL_APP"); + String title = new String(this.getTitle()); + if (viewtitle != null) + { + title = viewtitle + " ( " + title + ")"; + } + else + { + if (title.indexOf("(View") > -1) + { + title = title.substring(0, title.indexOf("(View")); + } + title += "(View " + viewSize + ")"; + } + + newaf.setTitle(title.toString()); + + newaf.viewport.setHistoryList(viewport.getHistoryList()); + newaf.viewport.setRedoList(viewport.getRedoList()); + return newaf; } + /** + * + * @return list of feature groups on the view + */ + public String[] getFeatureGroups() + { + FeatureRenderer fr = null; + if (alignPanel != null + && (fr = alignPanel.getFeatureRenderer()) != null) + { + List gps = fr.getFeatureGroups(); + String[] _gps = gps.toArray(new String[gps.size()]); + return _gps; + } + return null; + } - String removeWhiteSpace(String colour) + /** + * get sequence feature groups that are hidden or shown + * + * @param visible + * true is visible + * @return list + */ + public String[] getFeatureGroupsOfState(boolean visible) { - StringBuffer sb = new StringBuffer(); - for (int i = 0; i < colour.length(); i++) + FeatureRenderer fr = null; + if (alignPanel != null + && (fr = alignPanel.getFeatureRenderer()) != null) { - if (Character.isWhitespace(colour.charAt(i))) - sb.append("%20"); - else - sb.append(colour.charAt(i)); + List gps = fr.getGroups(visible); + String[] _gps = gps.toArray(new String[gps.size()]); + return _gps; } + return null; + } - return sb.toString(); + /** + * Change the display state for the given feature groups + * + * @param groups + * list of group strings + * @param state + * visible or invisible + */ + public void setFeatureGroupState(String[] groups, boolean state) + { + FeatureRenderer fr = null; + this.sequenceFeatures.setState(true); + viewport.setShowSequenceFeatures(true); + if (alignPanel != null + && (fr = alignPanel.getFeatureRenderer()) != null) + { + + fr.setGroupVisibility(Arrays.asList(groups), state); + alignPanel.seqPanel.seqCanvas.repaint(); + if (alignPanel.overviewPanel != null) + { + alignPanel.overviewPanel.updateOverviewImage(); + } + } + } + + public void seqLimits_itemStateChanged() + { + viewport.setShowJVSuffix(seqLimits.getState()); + alignPanel.fontChanged(); + alignPanel.paintAlignment(true); } + protected void colourTextMenuItem_actionPerformed() + { + viewport.setColourText(colourTextMenuItem.getState()); + alignPanel.paintAlignment(true); + } - String appendProtocol(String url) + protected void displayNonconservedMenuItem_actionPerformed() + { + viewport.setShowUnconserved(displayNonconservedMenuItem.getState()); + alignPanel.paintAlignment(true); + } + + protected void wrapMenuItem_actionPerformed() + { + viewport.setWrapAlignment(wrapMenuItem.getState()); + alignPanel.setWrapAlignment(wrapMenuItem.getState()); + scaleAbove.setEnabled(wrapMenuItem.getState()); + scaleLeft.setEnabled(wrapMenuItem.getState()); + scaleRight.setEnabled(wrapMenuItem.getState()); + alignPanel.paintAlignment(true); + } + + public void overviewMenuItem_actionPerformed() { - try{ - new URL(url); - }catch(java.net.MalformedURLException ex) + if (alignPanel.overviewPanel != null) { - url = viewport.applet.getCodeBase()+url; + return; } - return url; + + Frame frame = new Frame(); + OverviewPanel overview = new OverviewPanel(alignPanel); + frame.add(overview); + // +50 must allow for applet frame window + jalview.bin.JalviewLite.addFrame(frame, MessageManager.formatMessage( + "label.overview_params", new String[] { this.getTitle() }), + overview.getPreferredSize().width, + overview.getPreferredSize().height + 50); + + frame.pack(); + final AlignmentPanel ap = alignPanel; + frame.addWindowListener(new WindowAdapter() + { + @Override + public void windowClosing(WindowEvent e) + { + if (ap != null) + { + ap.setOverviewPanel(null); + } + }; + }); + + alignPanel.setOverviewPanel(overview); + } - public void closeMenuItem_actionPerformed() + @Override + public void changeColour(ColourSchemeI cs) { - PaintRefresher.components.remove(viewport.alignment); - if(PaintRefresher.components.size()==0 && viewport.applet==null) - System.exit(0); + viewport.setGlobalColourScheme(cs); - this.dispose(); + alignPanel.paintAlignment(true); } - Stack historyList = new Stack(); - Stack redoList = new Stack(); + protected void modifyPID_actionPerformed() + { + if (viewport.getAbovePIDThreshold() + && viewport.getGlobalColourScheme() != null) + { + SliderPanel.setPIDSliderSource(alignPanel, + viewport.getResidueShading(), alignPanel.getViewName()); + SliderPanel.showPIDSlider(); + } + } - void updateEditMenuBar() + protected void modifyConservation_actionPerformed() { - if (historyList.size() > 0) + if (viewport.getConservationSelected() + && viewport.getGlobalColourScheme() != null) { - undoMenuItem.setEnabled(true); - HistoryItem hi = (HistoryItem) historyList.peek(); - undoMenuItem.setLabel("Undo " + hi.getDescription()); + SliderPanel.setConservationSlider(alignPanel, + viewport.getResidueShading(), alignPanel.getViewName()); + SliderPanel.showConservationSlider(); + } + } + + protected void conservationMenuItem_actionPerformed() + { + boolean selected = conservationMenuItem.getState(); + modifyConservation.setEnabled(selected); + viewport.setConservationSelected(selected); + + // viewport.setAbovePIDThreshold(false); + // abovePIDThreshold.setState(false); + + changeColour(viewport.getGlobalColourScheme()); + + if (selected) + { + modifyConservation_actionPerformed(); } else { - undoMenuItem.setEnabled(false); - undoMenuItem.setLabel("Undo"); + SliderPanel.hideConservationSlider(); } + } + + public void abovePIDThreshold_actionPerformed() + { + boolean selected = abovePIDThreshold.getState(); + modifyPID.setEnabled(selected); + viewport.setAbovePIDThreshold(selected); + // conservationMenuItem.setState(false); + // viewport.setConservationSelected(false); + + changeColour(viewport.getGlobalColourScheme()); - if (redoList.size() > 0) + if (selected) { - redoMenuItem.setEnabled(true); - HistoryItem hi = (HistoryItem) redoList.peek(); - redoMenuItem.setLabel("Redo " + hi.getDescription()); + modifyPID_actionPerformed(); } else { - redoMenuItem.setEnabled(false); - redoMenuItem.setLabel("Redo"); + SliderPanel.hidePIDSlider(); } } - public void addHistoryItem(HistoryItem hi) + public void sortPairwiseMenuItem_actionPerformed() { - historyList.push(hi); - redoList.clear(); - updateEditMenuBar(); + SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray(); + AlignmentSorter.sortByPID(viewport.getAlignment(), viewport + .getAlignment().getSequenceAt(0), null); + + addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder, + viewport.getAlignment())); + alignPanel.paintAlignment(true); } - protected void undoMenuItem_actionPerformed() + public void sortIDMenuItem_actionPerformed() { - HistoryItem nh,hi = (HistoryItem) historyList.pop(); - redoList.push(nh=new HistoryItem(hi.getDescription(), viewport.alignment, - HistoryItem.HIDE)); - if (hi.alColumnChanges!=null) - nh.alColumnChanges=hi.alColumnChanges.getInverse(); - restoreHistoryItem(hi); - viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences()); + SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray(); + AlignmentSorter.sortByID(viewport.getAlignment()); + addHistoryItem(new OrderCommand("ID Sort", oldOrder, + viewport.getAlignment())); + alignPanel.paintAlignment(true); } - protected void redoMenuItem_actionPerformed() + public void sortLengthMenuItem_actionPerformed() { - HistoryItem nh,hi = (HistoryItem) redoList.pop(); - historyList.push(nh=new HistoryItem(hi.getDescription(), viewport.alignment, - HistoryItem.HIDE)); - if (hi.alColumnChanges!=null) - nh.alColumnChanges=hi.alColumnChanges.getInverse(); - restoreHistoryItem(hi); - updateEditMenuBar(); - viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences()); + SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray(); + AlignmentSorter.sortByLength(viewport.getAlignment()); + addHistoryItem(new OrderCommand("Length Sort", oldOrder, + viewport.getAlignment())); + alignPanel.paintAlignment(true); } - // used by undo and redo - void restoreHistoryItem(HistoryItem hi) + public void sortGroupMenuItem_actionPerformed() { - hi.restore(viewport.getColumnSelection()); - updateEditMenuBar(); + SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray(); + AlignmentSorter.sortByGroup(viewport.getAlignment()); + addHistoryItem(new OrderCommand("Group Sort", oldOrder, + viewport.getAlignment())); + alignPanel.paintAlignment(true); - viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences()); } - public void moveSelectedSequences(boolean up) + public void removeRedundancyMenuItem_actionPerformed() { - SequenceGroup sg = viewport.getSelectionGroup(); - if (sg == null) + new RedundancyPanel(alignPanel); + } + + public void pairwiseAlignmentMenuItem_actionPerformed() + { + if (viewport.getSelectionGroup() != null + && viewport.getSelectionGroup().getSize() > 1) { - return; + Frame frame = new Frame(); + frame.add(new PairwiseAlignPanel(alignPanel)); + jalview.bin.JalviewLite.addFrame(frame, + MessageManager.getString("action.pairwise_alignment"), 600, + 500); } + } - if (up) + public void PCAMenuItem_actionPerformed() + { + // are the sequences aligned? + if (!viewport.getAlignment().isAligned(false)) { - for (int i = 1; i < viewport.alignment.getHeight(); i++) - { - SequenceI seq = viewport.alignment.getSequenceAt(i); - if (!sg.getSequences(false).contains(seq)) - { - continue; - } - - SequenceI temp = viewport.alignment.getSequenceAt(i - 1); - if (sg.getSequences(false).contains(temp)) - { - continue; - } + SequenceI current; + int Width = viewport.getAlignment().getWidth(); - viewport.alignment.getSequences().setElementAt(temp, i); - viewport.alignment.getSequences().setElementAt(seq, i - 1); - } - } - else - { - for (int i = viewport.alignment.getHeight() - 2; i > -1; i--) + for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++) { - SequenceI seq = viewport.alignment.getSequenceAt(i); - if (!sg.getSequences(true).contains(seq)) - { - continue; - } + current = viewport.getAlignment().getSequenceAt(i); - SequenceI temp = viewport.alignment.getSequenceAt(i + 1); - if (sg.getSequences(true).contains(temp)) + if (current.getLength() < Width) { - continue; + current.insertCharAt(Width - 1, viewport.getGapCharacter()); } - - viewport.alignment.getSequences().setElementAt(temp, i); - viewport.alignment.getSequences().setElementAt(seq, i + 1); } + alignPanel.paintAlignment(true); } - alignPanel.repaint(); - } - - static StringBuffer copiedSequences; - static Vector copiedHiddenColumns; - protected void copy_actionPerformed() - { - if (viewport.getSelectionGroup() == null) + if ((viewport.getSelectionGroup() != null + && viewport.getSelectionGroup().getSize() < 4 && viewport + .getSelectionGroup().getSize() > 0) + || viewport.getAlignment().getHeight() < 4) { return; } - SequenceGroup sg = viewport.getSelectionGroup(); - copiedSequences = new StringBuffer(); - Hashtable orderedSeqs = new Hashtable(); - for (int i = 0; i < sg.getSize(false); i++) + try + { + new PCAPanel(viewport); + } catch (java.lang.OutOfMemoryError ex) { - SequenceI seq = sg.getSequenceAt(i); - int index = viewport.alignment.findIndex(seq); - orderedSeqs.put(index + "", seq); } - int index = 0, startRes, endRes; - char ch; + } - if (viewport.hasHiddenColumns && viewport.getSelectionGroup() != null) - { - copiedHiddenColumns = new Vector(); - int hiddenOffset = viewport.getSelectionGroup().getStartRes(); - for (int i = 0; i < viewport.getColumnSelection().getHiddenColumns().size(); - i++) - { - int[] region = (int[]) - viewport.getColumnSelection().getHiddenColumns().elementAt(i); + public void averageDistanceTreeMenuItem_actionPerformed() + { + NewTreePanel("AV", "PID", "Average distance tree using PID"); + } - copiedHiddenColumns.addElement(new int[] - {region[0] - hiddenOffset, - region[1] - hiddenOffset}); - } - } - else - copiedHiddenColumns = null; + public void neighbourTreeMenuItem_actionPerformed() + { + NewTreePanel("NJ", "PID", "Neighbour joining tree using PID"); + } + + protected void njTreeBlosumMenuItem_actionPerformed() + { + NewTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62"); + } + protected void avTreeBlosumMenuItem_actionPerformed() + { + NewTreePanel("AV", "BL", "Average distance tree using BLOSUM62"); + } - for (int i = 0; i < sg.getSize(false); i++) + void NewTreePanel(String type, String pwType, String title) + { + // are the sequences aligned? + if (!viewport.getAlignment().isAligned(false)) { - SequenceI seq = null; + SequenceI current; + int Width = viewport.getAlignment().getWidth(); + + for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++) + { + current = viewport.getAlignment().getSequenceAt(i); - while (seq == null) + if (current.getLength() < Width) { - if (orderedSeqs.containsKey(index + "")) - { - seq = (SequenceI) orderedSeqs.get(index + ""); - index++; - - break; - } - else - { - index++; - } + current.insertCharAt(Width - 1, viewport.getGapCharacter()); } + } + alignPanel.paintAlignment(true); - //FIND START RES - //Returns residue following index if gap - startRes = seq.findPosition(sg.getStartRes()); - - //FIND END RES - //Need to find the residue preceeding index if gap - endRes = 0; + } - for (int j = 0; j < sg.getEndRes()+1 && j < seq.getLength(); j++) - { - ch = seq.getCharAt(j); - if (!jalview.util.Comparison.isGap( (ch))) - { - endRes++; - } - } + if ((viewport.getSelectionGroup() != null && viewport + .getSelectionGroup().getSize() > 1) + || (viewport.getAlignment().getHeight() > 1)) + { + final TreePanel tp = new TreePanel(alignPanel, type, pwType); - if(endRes>0) - { - endRes += seq.getStart() -1; - } + addTreeMenuItem(tp, title); - copiedSequences.append(seq.getName() + "\t" + - startRes + "\t" + - endRes + "\t" + - seq.getSequence(sg.getStartRes(), - sg.getEndRes() + 1) + "\n"); + jalview.bin.JalviewLite.addFrame(tp, title, 600, 500); } + } + void loadTree_actionPerformed() + { + CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this); + cap.setText(MessageManager.getString("label.paste_newick_tree_file")); + cap.setTreeImport(); + Frame frame = new Frame(); + frame.add(cap); + jalview.bin.JalviewLite.addFrame(frame, + MessageManager.getString("label.paste_newick_file"), 400, 300); } - protected void pasteNew_actionPerformed() + public void loadTree(jalview.io.NewickFile tree, String treeFile) { - paste(true); + TreePanel tp = new TreePanel(alignPanel, treeFile, + MessageManager.getString("label.load_tree_from_file"), tree); + jalview.bin.JalviewLite.addFrame(tp, treeFile, 600, 500); + addTreeMenuItem(tp, treeFile); } - protected void pasteThis_actionPerformed() + /** + * sort the alignment using the given treePanel + * + * @param treePanel + * tree used to sort view + * @param title + * string used for undo event name + */ + public void sortByTree(TreePanel treePanel, String title) { - addHistoryItem(new HistoryItem("Paste Sequences", viewport.alignment, - HistoryItem.PASTE)); - paste(false); + SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray(); + AlignmentSorter + .sortByTree(viewport.getAlignment(), treePanel.getTree()); + // addHistoryItem(new HistoryItem("Sort", viewport.alignment, + // HistoryItem.SORT)); + addHistoryItem(new OrderCommand(MessageManager.formatMessage( + "label.order_by_params", new String[] { title }), oldOrder, + viewport.getAlignment())); + alignPanel.paintAlignment(true); } - void paste(boolean newAlignment) + /** + * Do any automatic reordering of the alignment and add the necessary bits to + * the menu structure for the new tree + * + * @param treePanel + * @param title + */ + protected void addTreeMenuItem(final TreePanel treePanel, + final String title) { - try + final MenuItem item = new MenuItem(title); + sortByTreeMenu.add(item); + item.addActionListener(new java.awt.event.ActionListener() { - if (copiedSequences == null) + @Override + public void actionPerformed(ActionEvent evt) { - return; + sortByTree(treePanel, title); // treePanel.getTitle()); } + }); - StringTokenizer st = new StringTokenizer(copiedSequences.toString()); - Vector seqs = new Vector(); - while (st.hasMoreElements()) + treePanel.addWindowListener(new WindowAdapter() + { + @Override + public void windowOpened(WindowEvent e) { - String name = st.nextToken(); - int start = Integer.parseInt(st.nextToken()); - int end = Integer.parseInt(st.nextToken()); - Sequence sequence = new Sequence(name, st.nextToken(), start, end); - - if (!newAlignment) + if (viewport.sortByTree) { - viewport.alignment.addSequence(sequence); - } - else - { - seqs.addElement(sequence); + sortByTree(treePanel, title); } + super.windowOpened(e); } - if (newAlignment) - { - SequenceI[] newSeqs = new SequenceI[seqs.size()]; - for (int i = 0; i < seqs.size(); i++) - { - newSeqs[i] = (SequenceI) seqs.elementAt(i); - } - - String newtitle = new String("Copied sequences"); - if (getTitle().startsWith("Copied sequences")) - { - newtitle = getTitle(); - } - else - { - newtitle = newtitle.concat("- from " + getTitle()); - } - AlignFrame af = new AlignFrame(new Alignment(newSeqs), - viewport.applet, - newtitle, - false); - if (copiedHiddenColumns != null) - { - for (int i = 0; i < copiedHiddenColumns.size(); i++) - { - int[] region = (int[]) copiedHiddenColumns.elementAt(i); - af.viewport.hideColumns(region[0], region[1]); - } - } - - - jalview.bin.JalviewLite.addFrame(af, newtitle, NEW_WINDOW_WIDTH, - NEW_WINDOW_HEIGHT); - } - else + @Override + public void windowClosing(WindowEvent e) { - viewport.setEndSeq(viewport.alignment.getHeight()); - viewport.alignment.getWidth(); - viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences()); - } + sortByTreeMenu.remove(item); + }; + }); + } + public boolean sortBy(AlignmentOrder alorder, String undoname) + { + SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray(); + if (viewport.applet.debug) + { + System.err.println("Sorting " + alorder.getOrder().size() + + " in alignment '" + getTitle() + "'"); } - catch (Exception ex) - {} // could be anything being pasted in here - + AlignmentSorter.sortBy(viewport.getAlignment(), alorder); + if (undoname != null) + { + addHistoryItem(new OrderCommand(undoname, oldOrder, + viewport.getAlignment())); + } + alignPanel.paintAlignment(true); + return true; } - protected void cut_actionPerformed() + protected void documentation_actionPerformed() { - copy_actionPerformed(); - delete_actionPerformed(); + alignPanel.av.applet.openJalviewHelpUrl(); } - protected void delete_actionPerformed() + protected void about_actionPerformed() { - addHistoryItem(new HistoryItem("Delete Sequences", viewport.alignment, - HistoryItem.HIDE)); - if (viewport.getSelectionGroup() == null) - { - return; - } - - SequenceGroup sg = viewport.getSelectionGroup(); - boolean allSequences = false; - if(sg.getSize(false)==viewport.alignment.getHeight()) - allSequences = true; - - for (int i = 0; i < sg.getSize(false); i++) + class AboutPanel extends Canvas { - SequenceI seq = sg.getSequenceAt(i); - int index = viewport.getAlignment().findIndex(seq); - seq.deleteChars(sg.getStartRes(), sg.getEndRes() + 1); - - // If the cut affects all sequences, remove highlighted columns - if (allSequences) - { - viewport.getColumnSelection().removeElements(sg.getStartRes(), - sg.getEndRes() + 1); - } + String version; + String builddate; - if (seq.getSequence().length() < 1) - { - viewport.getAlignment().deleteSequence(seq); - } - else + public AboutPanel(String version, String builddate) { - viewport.getAlignment().getSequences().setElementAt(seq, index); + this.version = version; + this.builddate = builddate; } - } - viewport.setSelectionGroup(null); - viewport.alignment.deleteGroup(sg); - viewport.resetSeqLimits(alignPanel.seqPanel.seqCanvas.getSize().height); - if (viewport.getAlignment().getHeight() < 1) - { - try + @Override + public void paint(Graphics g) { - this.setVisible(false); + g.setColor(Color.white); + g.fillRect(0, 0, getSize().width, getSize().height); + g.setFont(new Font("Helvetica", Font.PLAIN, 12)); + FontMetrics fm = g.getFontMetrics(); + int fh = fm.getHeight(); + int y = 5, x = 7; + g.setColor(Color.black); + // TODO: update this text for each release or centrally store it for + // lite and application + g.setFont(new Font("Helvetica", Font.BOLD, 14)); + g.drawString(MessageManager.formatMessage( + "label.jalviewLite_release", new String[] { version }), x, + y += fh); + g.setFont(new Font("Helvetica", Font.BOLD, 12)); + g.drawString(MessageManager.formatMessage( + "label.jaview_build_date", new String[] { builddate }), x, + y += fh); + g.setFont(new Font("Helvetica", Font.PLAIN, 12)); + g.drawString(MessageManager.getString("label.jalview_authors_1"), + x, y += fh * 1.5); + g.drawString(MessageManager.getString("label.jalview_authors_2"), + x + 50, y += fh + 8); + g.drawString( + MessageManager.getString("label.jalview_dev_managers"), x, + y += fh); + g.drawString(MessageManager + .getString("label.jalview_distribution_lists"), x, y += fh); + g.drawString(MessageManager.getString("label.jalview_please_cite"), + x, y += fh + 8); + g.drawString( + MessageManager.getString("label.jalview_cite_1_authors"), + x, y += fh); + g.drawString( + MessageManager.getString("label.jalview_cite_1_title"), x, + y += fh); + g.drawString(MessageManager.getString("label.jalview_cite_1_ref"), + x, y += fh); } - catch (Exception ex) - {} } - viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences()); - - } - protected void deleteGroups_actionPerformed() - { - viewport.alignment.deleteAllGroups(); - viewport.setSelectionGroup(null); + Frame frame = new Frame(); + frame.add(new AboutPanel(JalviewLite.getVersion(), JalviewLite + .getBuildDate())); + jalview.bin.JalviewLite.addFrame(frame, + MessageManager.getString("label.jalview"), 580, 220); - alignPanel.repaint(); } - public void selectAllSequenceMenuItem_actionPerformed() + public void showURL(String url, String target) { - SequenceGroup sg = new SequenceGroup(); - for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++) + if (viewport.applet == null) { - sg.addSequence(viewport.getAlignment().getSequenceAt(i), false); + System.out.println("Not running as applet - no browser available."); } - sg.setEndRes(viewport.alignment.getWidth()-1); - viewport.setSelectionGroup(sg); - alignPanel.repaint(); - PaintRefresher.Refresh(null, viewport.alignment); - } - - public void deselectAllSequenceMenuItem_actionPerformed() - { - if(viewport.cursorMode) + else { - alignPanel.seqPanel.keyboardNo1=null; - alignPanel.seqPanel.keyboardNo2=null; + viewport.applet.showURL(url, target); } - viewport.setSelectionGroup(null); - viewport.getColumnSelection().clear(); - viewport.setSelectionGroup(null); - alignPanel.idPanel.idCanvas.searchResults = null; - alignPanel.seqPanel.seqCanvas.highlightSearchResults(null); - alignPanel.repaint(); - PaintRefresher.Refresh(null, viewport.alignment); } - public void invertSequenceMenuItem_actionPerformed() - { - SequenceGroup sg = viewport.getSelectionGroup(); - for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++) - { - sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false); - } + // //////////////////////////////////////////////////////////////////////////////// + // JBuilder Graphics here - PaintRefresher.Refresh(null, viewport.alignment); - } + MenuBar alignFrameMenuBar = new MenuBar(); - public void remove2LeftMenuItem_actionPerformed() - { - ColumnSelection colSel = viewport.getColumnSelection(); - if (colSel.size() > 0) - { - HistoryItem edit; - addHistoryItem(edit=new HistoryItem("Remove Left", viewport.alignment, - HistoryItem.HIDE)); - int min = colSel.getMin(); - viewport.getAlignment().trimLeft(min); - colSel.compensateForEdit(0, min); - edit.addShift(0, min); - if (viewport.getSelectionGroup() != null) - { - viewport.getSelectionGroup().adjustForRemoveLeft(min); - } + Menu fileMenu = new Menu(MessageManager.getString("action.file")); + + MenuItem loadApplication = new MenuItem( + MessageManager.getString("label.view_full_application")); + + MenuItem loadTree = new MenuItem( + MessageManager.getString("label.load_associated_tree")); + + MenuItem loadAnnotations = new MenuItem( + MessageManager.getString("label.load_features_annotations")); + + MenuItem outputFeatures = new MenuItem( + MessageManager.getString("label.export_features")); + + MenuItem outputAnnotations = new MenuItem( + MessageManager.getString("label.export_annotations")); + + MenuItem closeMenuItem = new MenuItem( + MessageManager.getString("action.close")); + + MenuItem selectAllSequenceMenuItem = new MenuItem( + MessageManager.getString("action.select_all")); + + MenuItem deselectAllSequenceMenuItem = new MenuItem( + MessageManager.getString("action.deselect_all")); + + MenuItem invertSequenceMenuItem = new MenuItem( + MessageManager.getString("action.invert_selection")); + + MenuItem remove2LeftMenuItem = new MenuItem(); + + MenuItem remove2RightMenuItem = new MenuItem(); + + MenuItem removeGappedColumnMenuItem = new MenuItem(); + + MenuItem removeAllGapsMenuItem = new MenuItem(); + + CheckboxMenuItem viewBoxesMenuItem = new CheckboxMenuItem(); + + CheckboxMenuItem viewTextMenuItem = new CheckboxMenuItem(); + + MenuItem sortPairwiseMenuItem = new MenuItem(); + + MenuItem sortIDMenuItem = new MenuItem(); + + MenuItem sortLengthMenuItem = new MenuItem(); + + MenuItem sortGroupMenuItem = new MenuItem(); - Vector groups = viewport.alignment.getGroups(); - for (int i = 0; i < groups.size(); i++) - { - SequenceGroup sg = (SequenceGroup) groups.elementAt(i); - if (!sg.adjustForRemoveLeft(min)) - { - viewport.alignment.deleteGroup(sg); - } - } - viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences()); - } - } + MenuItem removeRedundancyMenuItem = new MenuItem(); - public void remove2RightMenuItem_actionPerformed() - { - ColumnSelection colSel = viewport.getColumnSelection(); - if (colSel.size() > 0) - { - addHistoryItem(new HistoryItem("Remove Right", viewport.alignment, - HistoryItem.HIDE)); - int max = colSel.getMax(); - viewport.getAlignment().trimRight(max); - - if (viewport.getSelectionGroup() != null) - { - viewport.getSelectionGroup().adjustForRemoveRight(max); - } + MenuItem pairwiseAlignmentMenuItem = new MenuItem(); - Vector groups = viewport.alignment.getGroups(); - for (int i = 0; i < groups.size(); i++) - { - SequenceGroup sg = (SequenceGroup) groups.elementAt(i); - if (!sg.adjustForRemoveRight(max)) - { - viewport.alignment.deleteGroup(sg); - } - } - viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences()); - } + MenuItem PCAMenuItem = new MenuItem(); - } + MenuItem averageDistanceTreeMenuItem = new MenuItem(); - public void removeGappedColumnMenuItem_actionPerformed() - { - HistoryItem edit; - addHistoryItem(edit=new HistoryItem("Remove Gapped Columns", - viewport.alignment, - HistoryItem.HIDE)); + MenuItem neighbourTreeMenuItem = new MenuItem(); - //This is to maintain viewport position on first residue - //of first sequence - SequenceI seq = viewport.alignment.getSequenceAt(0); - int startRes = seq.findPosition(viewport.startRes); + BorderLayout borderLayout1 = new BorderLayout(); - viewport.getAlignment().removeGaps(); - - viewport.setStartRes(seq.findIndex(startRes)-1); + public Label statusBar = new Label(); - viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences()); - } + MenuItem clustalColour = new MenuItem(); - public void removeAllGapsMenuItem_actionPerformed() - { - // TODO: hidden regions should not be touched by removeAllGaps - a minimal number of gaps will remain in alignment segments containing uneven length subsequences - // TODO: columnSelection.compensateforedits should be called (and passed to history item) - HistoryItem editgaps; - addHistoryItem(editgaps=new HistoryItem("Remove Gaps", viewport.alignment, - HistoryItem.HIDE)); + MenuItem zappoColour = new MenuItem(); - //This is to maintain viewport position on first residue - //of first sequence - SequenceI seq = viewport.alignment.getSequenceAt(0); - int startRes = seq.findPosition(viewport.startRes); + MenuItem taylorColour = new MenuItem(); - SequenceI current; - Vector seqs=null; + MenuItem hydrophobicityColour = new MenuItem(); - int start=0, end = viewport.alignment.getWidth(); + MenuItem helixColour = new MenuItem(); - if (viewport.getSelectionGroup() != null - && viewport.getSelectionGroup().getSequences(false) != null - && viewport.getSelectionGroup().getSize(false)>0) - { - seqs = viewport.getSelectionGroup().getSequences(true); - start = viewport.getSelectionGroup().getStartRes(); - end = viewport.getSelectionGroup().getEndRes()+1; - } - else - seqs = viewport.alignment.getSequences(); - - /* Commented out regions below are partial implementation of todo above. - * divide start,end into visible chunks, and for each: - int diff=end-start+1; - int diffmax=0; - int dr[] = new int[seqs.size()]; - */ - for (int i = 0; i < seqs.size(); i++) - { - current = (SequenceI) seqs.elementAt(i); - //dr[i]= - current.removeGaps(start, end); - /*if (d0) { - // record shift for history. - editgaps.addShift(start, diff); - if (viewport.hasHiddenColumns && diffmax>diff) { - // pad sequence - StringBuffer gaps=new StringBuffer(diffmax); - for (int i=0,j=diffmax-diff; i0) { - String sq = current.getSequence(); - current.setSequence(sq.substring(0, hcend-dr[i])+gaps.substring(0, dr[i]-diff)+sq.substring()); - } - } - } - }*/ - - viewport.setStartRes(seq.findIndex(startRes)-1); - viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences()); - } + MenuItem strandColour = new MenuItem(); - public void alignmentChanged() - { - viewport.alignment.padGaps(); - if(viewport.autocalculateConsensus) - { - viewport.updateConsensus(); - viewport.updateConservation(); - } + MenuItem turnColour = new MenuItem(); - resetAllColourSchemes(); - if(alignPanel.overviewPanel!=null) - alignPanel.overviewPanel.updateOverviewImage(); + MenuItem buriedColour = new MenuItem(); - viewport.alignment.adjustSequenceAnnotations(); - alignPanel.repaint(); - } + MenuItem purinePyrimidineColour = new MenuItem(); - void resetAllColourSchemes() - { - ColourSchemeI cs = viewport.globalColourScheme; - if(cs!=null) - { - if (cs instanceof ClustalxColourScheme) - { - ( (ClustalxColourScheme) viewport.getGlobalColourScheme()). - resetClustalX(viewport.alignment.getSequences(), - viewport.alignment.getWidth()); - } + // MenuItem RNAInteractionColour = new MenuItem(); - cs.setConsensus(viewport.vconsensus); - if (cs.conservationApplied()) - { - Alignment al = (Alignment) viewport.alignment; - Conservation c = new Conservation("All", - ResidueProperties.propHash, 3, - al.getSequences(), 0, - al.getWidth() - 1); - c.calculate(); - c.verdict(false, viewport.ConsPercGaps); + MenuItem RNAHelixColour = new MenuItem(); - cs.setConservation(c); - } - } + MenuItem userDefinedColour = new MenuItem(); - int s, sSize = viewport.alignment.getGroups().size(); - for(s=0; s 1) + if (reallyEmbedded) { - Frame frame = new Frame(); - frame.add(new PairwiseAlignPanel(alignPanel)); - jalview.bin.JalviewLite.addFrame(frame, "Pairwise Alignment", 600, 500); + embedAlignFrameInApplet(viewport.applet); + } + else + { + // ////// + // test and embed menu bar if necessary. + // + if (embedMenuIfNeeded(alignPanel)) + { + /* + * adjust for status bar height too. ? pointless as overridden by layout + * manager + */ + alignPanel.setSize(getSize().width, + getSize().height - statusBar.getHeight()); + } + add(statusBar, BorderLayout.SOUTH); + add(alignPanel, BorderLayout.CENTER); + // and register with the applet so it can pass external API calls to us + jalview.bin.JalviewLite.addFrame(this, this.getTitle(), frameWidth, + frameHeight); } } - public void PCAMenuItem_actionPerformed() + /** + * Add the components of this AlignFrame to the applet container. + * + * @param theApplet + */ + public void embedAlignFrameInApplet(final JalviewLite theApplet) { - //are the sequences aligned? - if (!viewport.alignment.isAligned()) + // //// + // Explicitly build the embedded menu panel for the on-page applet + // + // view cannot be closed if its actually on the page + fileMenu.remove(closeMenuItem); + fileMenu.remove(3); // Remove Separator + // construct embedded menu, using default font + embeddedMenu = makeEmbeddedPopupMenu(alignFrameMenuBar, false, false); + // and actually add the components to the applet area + theApplet.setLayout(new BorderLayout()); + theApplet.add(embeddedMenu, BorderLayout.NORTH); + theApplet.add(statusBar, BorderLayout.SOUTH); + // TODO should size be left to the layout manager? + alignPanel.setSize(theApplet.getSize().width, + theApplet.getSize().height - embeddedMenu.getHeight() + - statusBar.getHeight()); + theApplet.add(alignPanel, BorderLayout.CENTER); + final AlignFrame me = this; + theApplet.addFocusListener(new FocusListener() { - SequenceI current; - int Width = viewport.getAlignment().getWidth(); - for (int i = 0; i < viewport.getAlignment().getSequences().size(); - i++) + @Override + public void focusLost(FocusEvent e) { - current = viewport.getAlignment().getSequenceAt(i); - - if (current.getLength() < Width) + if (theApplet.currentAlignFrame == me) { - current.insertCharAt(Width - 1, viewport.getGapCharacter()); + theApplet.currentAlignFrame = null; } } - alignPanel.repaint(); - } - if ( (viewport.getSelectionGroup() != null && - viewport.getSelectionGroup().getSize(false) < 4 && - viewport.getSelectionGroup().getSize(false) > 0) - || viewport.getAlignment().getHeight() < 4) - { - return; - } + @Override + public void focusGained(FocusEvent e) + { + theApplet.currentAlignFrame = me; + } + }); + theApplet.validate(); + } + /** + * create a new binding between structures in an existing jmol viewer instance + * and an alignpanel with sequences that have existing PDBFile entries. Note, + * this does not open a new Jmol window, or modify the display of the + * structures in the original jmol window. Note This method doesn't work + * without an additional javascript library to exchange messages between the + * distinct applets. See http://issues.jalview.org/browse/JAL-621 + * + * @param viewer + * JmolViewer instance + * @param sequenceIds + * - sequence Ids to search for associations + */ + public SequenceStructureBinding addStructureViewInstance( + Object jmolviewer, String[] sequenceIds) + { + Viewer viewer = null; try { - new PCAPanel(viewport); + viewer = (Viewer) jmolviewer; + } catch (ClassCastException ex) + { + System.err.println("Unsupported viewer object :" + + jmolviewer.getClass()); } - catch (java.lang.OutOfMemoryError ex) + if (viewer == null) { + System.err.println("Can't use this object as a structure viewer:" + + jmolviewer.getClass()); + return null; } - - } - - public void averageDistanceTreeMenuItem_actionPerformed() - { - NewTreePanel("AV", "PID", "Average distance tree using PID"); - } - - public void neighbourTreeMenuItem_actionPerformed() - { - NewTreePanel("NJ", "PID", "Neighbour joining tree using PID"); - } - - protected void njTreeBlosumMenuItem_actionPerformed() - { - NewTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62"); - } - - protected void avTreeBlosumMenuItem_actionPerformed() - { - NewTreePanel("AV", "BL", "Average distance tree using BLOSUM62PID"); - } - - void NewTreePanel(String type, String pwType, String title) - { - //are the sequences aligned? - if (!viewport.alignment.isAligned()) + SequenceI[] seqs = null; + if (sequenceIds == null || sequenceIds.length == 0) { - SequenceI current; - int Width = viewport.getAlignment().getWidth(); - - for (int i = 0; i < viewport.getAlignment().getSequences().size(); - i++) + seqs = viewport.getAlignment().getSequencesArray(); + } + else + { + Vector sqi = new Vector(); + AlignmentI al = viewport.getAlignment(); + for (int sid = 0; sid < sequenceIds.length; sid++) { - current = viewport.getAlignment().getSequenceAt(i); - - if (current.getLength() < Width) + SequenceI sq = al.findName(sequenceIds[sid]); + if (sq != null) { - current.insertCharAt(Width - 1, viewport.getGapCharacter()); + sqi.addElement(sq); } } - alignPanel.repaint(); - + if (sqi.size() > 0) + { + seqs = new SequenceI[sqi.size()]; + for (int sid = 0, sSize = sqi.size(); sid < sSize; sid++) + { + seqs[sid] = (SequenceI) sqi.elementAt(sid); + } + } + else + { + return null; + } } - - if ( (viewport.getSelectionGroup() != null && - viewport.getSelectionGroup().getSize(false) > 1) - || (viewport.getSelectionGroup() == null - && viewport.alignment.getHeight() > 1)) - { - final TreePanel tp = new TreePanel(viewport, - type, - pwType); - - addTreeMenuItem(tp, title); - - jalview.bin.JalviewLite.addFrame(tp, title, 600, 500); + AAStructureBindingModel jmv = null; + // TODO: search for a jmv that involves viewer + if (jmv == null) + { // create a new viewer/jalview binding. + jmv = new ExtJmol(viewer, alignPanel, new SequenceI[][] { seqs }); } - } + return jmv; - void loadTree_actionPerformed() - { - CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this); - cap.setText("Paste your Newick tree file here."); - cap.treeImport = true; - Frame frame = new Frame(); - frame.add(cap); - jalview.bin.JalviewLite.addFrame(frame, "Paste Newick file ", 400, 300); } - public void loadTree(jalview.io.NewickFile tree, String treeFile) + /** + * bind a pdb file to a sequence in the current view + * + * @param sequenceId + * - sequenceId within the dataset. + * @param pdbEntryString + * - the short name for the PDB file + * @param pdbFile + * - pdb file - either a URL or a valid PDB file. + * @return true if binding was as success TODO: consider making an exception + * structure for indicating when PDB parsing or sequenceId location + * fails. + */ + public boolean addPdbFile(String sequenceId, String pdbEntryString, + String pdbFile) { - TreePanel tp = new TreePanel(viewport, - treeFile, - "From File - ", - tree); - jalview.bin.JalviewLite.addFrame(tp, treeFile, 600, 500); - addTreeMenuItem(tp, treeFile); + SequenceI toaddpdb = viewport.getAlignment().findName(sequenceId); + boolean needtoadd = false; + if (toaddpdb != null) + { + Vector pdbe = toaddpdb.getAllPDBEntries(); + PDBEntry pdbentry = null; + if (pdbe != null && pdbe.size() > 0) + { + for (int pe = 0, peSize = pdbe.size(); pe < peSize; pe++) + { + pdbentry = (PDBEntry) pdbe.elementAt(pe); + if (!pdbentry.getId().equals(pdbEntryString) + && !pdbentry.getFile().equals(pdbFile)) + { + pdbentry = null; + } + else + { + continue; + } + } + } + if (pdbentry == null) + { + pdbentry = new PDBEntry(); + pdbentry.setId(pdbEntryString); + pdbentry.setFile(pdbFile); + needtoadd = true; // add this new entry to sequence. + } + // resolve data source + // TODO: this code should be a refactored to an io package + DataSourceType protocol = AppletFormatAdapter.resolveProtocol( + pdbFile, FileFormat.PDB); + if (protocol == null) + { + return false; + } + if (needtoadd) + { + pdbentry.setProperty("protocol", protocol); + toaddpdb.addPDBId(pdbentry); + alignPanel.getStructureSelectionManager() + .registerPDBEntry(pdbentry); + } + } + return true; } - void addTreeMenuItem(final TreePanel treePanel, String title) + private Object[] cleanSeqChainArrays(SequenceI[] seqs, String[] chains) { - final MenuItem item = new MenuItem(title); - sortByTreeMenu.add(item); - item.addActionListener(new java.awt.event.ActionListener() + if (seqs != null) { - public void actionPerformed(ActionEvent evt) + Vector sequences = new Vector(); + for (int i = 0; i < seqs.length; i++) { - addHistoryItem(new HistoryItem("Sort", viewport.alignment, - HistoryItem.SORT)); - AlignmentSorter.sortByTree(viewport.getAlignment(), treePanel.getTree()); - alignPanel.repaint(); + if (seqs[i] != null) + { + sequences.addElement(new Object[] { seqs[i], + (chains != null) ? chains[i] : null }); + } } - }); - - treePanel.addWindowListener(new WindowAdapter() - { - public void windowClosing(WindowEvent e) + seqs = new SequenceI[sequences.size()]; + chains = new String[sequences.size()]; + for (int i = 0, isize = sequences.size(); i < isize; i++) { - sortByTreeMenu.remove(item); - }; - }); - } + Object[] oj = (Object[]) sequences.elementAt(i); + + seqs[i] = (SequenceI) oj[0]; + chains[i] = (String) oj[1]; + } + } + return new Object[] { seqs, chains }; - protected void documentation_actionPerformed() - { - showURL("http://www.jalview.org/help.html", "HELP"); } - protected void about_actionPerformed() + public void newStructureView(JalviewLite applet, PDBEntry pdb, + SequenceI[] seqs, String[] chains, DataSourceType protocol) { - - class AboutPanel extends Canvas + // Scrub any null sequences from the array + Object[] sqch = cleanSeqChainArrays(seqs, chains); + seqs = (SequenceI[]) sqch[0]; + chains = (String[]) sqch[1]; + if (seqs == null || seqs.length == 0) { - String version; - public AboutPanel(String version) - { this.version = version; } - - public void paint(Graphics g) + System.err + .println("JalviewLite.AlignFrame:newStructureView: No sequence to bind structure to."); + } + if (protocol == null) + { + String sourceType = (String) pdb.getProperty("protocol"); + try { - g.setColor(Color.white); - g.fillRect(0, 0, getSize().width, getSize().height); - g.setFont(new Font("Helvetica", Font.PLAIN, 12)); - FontMetrics fm = g.getFontMetrics(); - int fh = fm.getHeight(); - int y = 5, x = 7; - g.setColor(Color.black); - g.setFont(new Font("Helvetica", Font.BOLD, 14)); - g.drawString("Jalview - Release "+version, 200, y += fh); - g.setFont(new Font("Helvetica", Font.PLAIN, 12)); - g.drawString("Authors: Michele Clamp, James Cuff, Steve Searle, Andrew Waterhouse, Jim Procter & Geoff Barton.", - x, y += fh * 2); - g.drawString("Current development managed by Andrew Waterhouse; Barton Group, University of Dundee.", - x, y += fh); - g.drawString( - "For any issues relating to Jalview, email help@jalview.org", x, - y += fh); - g.drawString("If you use JalView, please cite:", x, y += fh + 8); - g.drawString("\"Clamp, M., Cuff, J., Searle, S. M. and Barton, G. J. (2004), The Jalview Java Alignment Editor\"", - x, y += fh); - g.drawString("Bioinformatics, 2004 20;426-7.", x, y += fh); + protocol = DataSourceType.valueOf(sourceType); + } catch (IllegalArgumentException e) + { + // ignore + } + if (protocol == null) + { + System.err.println("Couldn't work out protocol to open structure: " + + pdb.getId()); + return; } } - - String version = "test"; - java.net.URL url = getClass().getResource("/.build_properties"); - if (url != null) + if (applet.useXtrnalSviewer) { - try + // register the association(s) and quit, don't create any windows. + if (StructureSelectionManager.getStructureSelectionManager(applet) + .setMapping(seqs, chains, pdb.getFile(), protocol) == null) + { + System.err.println("Failed to map " + pdb.getFile() + " (" + + protocol + ") to any sequences"); + } + return; + } + if (applet.isAlignPdbStructures() && applet.jmolAvailable) + { + // can only do alignments with Jmol + // find the last jmol window assigned to this alignment + AppletJmol ajm = null, tajm; + Vector jmols = applet.getAppletWindow(AppletJmol.class); + for (int i = 0, iSize = jmols.size(); i < iSize; i++) { - BufferedReader reader = new BufferedReader(new InputStreamReader( - url.openStream())); - String line; - while ( (line = reader.readLine()) != null) + tajm = (AppletJmol) jmols.elementAt(i); + if (tajm.ap.alignFrame == this) { - if (line.indexOf("VERSION") > -1) - { - version = line.substring(line.indexOf("=") + 1); - } + ajm = tajm; + break; } } - catch (Exception ex) + if (ajm != null) { - ex.printStackTrace(); + System.err + .println("Incremental adding and aligning structure to existing Jmol view not yet implemented."); + // try and add the pdb structure + // ajm.addS + ajm = null; } } - - - Frame frame = new Frame(); - frame.add(new AboutPanel(version)); - jalview.bin.JalviewLite.addFrame(frame, "Jalview", 580, 200); - - } - - public void showURL(String url, String target) - { - if (viewport.applet == null) + // otherwise, create a new window + if (applet.jmolAvailable) { - System.out.println("Not running as applet - no browser available."); + new AppletJmol(pdb, seqs, chains, alignPanel, + protocol); + applet.lastFrameX += 40; + applet.lastFrameY += 40; } else { - try - { - System.out.println("Show url: "+url); - viewport.applet.getAppletContext().showDocument(new java.net.URL(url), - target); - } - catch (Exception ex) - { - ex.printStackTrace(); - } - } - } - - - ////////////////////////////////////////////////////////////////////////////////// - //JBuilder Graphics here - - protected MenuBar alignFrameMenuBar = new MenuBar(); - protected Menu fileMenu = new Menu("File"); - protected MenuItem loadApplication = new MenuItem("View in Full Application"); - protected MenuItem loadTree = new MenuItem("Load Associated Tree"); - protected MenuItem closeMenuItem = new MenuItem("Close"); - protected Menu editMenu = new Menu("Edit"); - protected Menu viewMenu = new Menu("View"); - protected Menu colourMenu = new Menu("Colour"); - protected Menu calculateMenu = new Menu("Calculate"); - protected MenuItem selectAllSequenceMenuItem = new MenuItem("Select all"); - protected MenuItem deselectAllSequenceMenuItem = new MenuItem("Deselect All"); - protected MenuItem invertSequenceMenuItem = new MenuItem("Invert Selection"); - protected MenuItem remove2LeftMenuItem = new MenuItem(); - protected MenuItem remove2RightMenuItem = new MenuItem(); - protected MenuItem removeGappedColumnMenuItem = new MenuItem(); - protected MenuItem removeAllGapsMenuItem = new MenuItem(); - protected CheckboxMenuItem viewBoxesMenuItem = new CheckboxMenuItem(); - protected CheckboxMenuItem viewTextMenuItem = new CheckboxMenuItem(); - protected MenuItem sortPairwiseMenuItem = new MenuItem(); - protected MenuItem sortIDMenuItem = new MenuItem(); - protected MenuItem sortGroupMenuItem = new MenuItem(); - protected MenuItem removeRedundancyMenuItem = new MenuItem(); - protected MenuItem pairwiseAlignmentMenuItem = new MenuItem(); - protected MenuItem PCAMenuItem = new MenuItem(); - protected MenuItem averageDistanceTreeMenuItem = new MenuItem(); - protected MenuItem neighbourTreeMenuItem = new MenuItem(); - BorderLayout borderLayout1 = new BorderLayout(); - public Label statusBar = new Label(); - protected Menu outputTextboxMenu = new Menu(); - protected MenuItem clustalColour = new MenuItem(); - protected MenuItem zappoColour = new MenuItem(); - protected MenuItem taylorColour = new MenuItem(); - protected MenuItem hydrophobicityColour = new MenuItem(); - protected MenuItem helixColour = new MenuItem(); - protected MenuItem strandColour = new MenuItem(); - protected MenuItem turnColour = new MenuItem(); - protected MenuItem buriedColour = new MenuItem(); - protected MenuItem userDefinedColour = new MenuItem(); - protected MenuItem PIDColour = new MenuItem(); - protected MenuItem BLOSUM62Colour = new MenuItem(); - MenuItem njTreeBlosumMenuItem = new MenuItem(); - MenuItem avDistanceTreeBlosumMenuItem = new MenuItem(); - protected CheckboxMenuItem annotationPanelMenuItem = new CheckboxMenuItem(); - protected CheckboxMenuItem colourTextMenuItem = new CheckboxMenuItem(); - MenuItem overviewMenuItem = new MenuItem(); - protected MenuItem undoMenuItem = new MenuItem(); - protected MenuItem redoMenuItem = new MenuItem(); - protected CheckboxMenuItem conservationMenuItem = new CheckboxMenuItem(); - MenuItem noColourmenuItem = new MenuItem(); - protected CheckboxMenuItem wrapMenuItem = new CheckboxMenuItem(); - protected CheckboxMenuItem renderGapsMenuItem = new CheckboxMenuItem(); - MenuItem findMenuItem = new MenuItem(); - Menu searchMenu = new Menu(); - protected CheckboxMenuItem abovePIDThreshold = new CheckboxMenuItem(); - protected MenuItem nucleotideColour = new MenuItem(); - MenuItem deleteGroups = new MenuItem(); - MenuItem delete = new MenuItem(); - MenuItem copy = new MenuItem(); - MenuItem cut = new MenuItem(); - Menu pasteMenu = new Menu(); - MenuItem pasteNew = new MenuItem(); - MenuItem pasteThis = new MenuItem(); - protected CheckboxMenuItem applyToAllGroups = new CheckboxMenuItem(); - protected MenuItem font = new MenuItem(); - protected CheckboxMenuItem scaleAbove = new CheckboxMenuItem(); - protected CheckboxMenuItem scaleLeft = new CheckboxMenuItem(); - protected CheckboxMenuItem scaleRight = new CheckboxMenuItem(); - MenuItem modifyPID = new MenuItem(); - MenuItem modifyConservation = new MenuItem(); - protected CheckboxMenuItem autoCalculate - = new CheckboxMenuItem("Autocalculate Consensus", true); - protected Menu sortByTreeMenu = new Menu(); - Menu sort = new Menu(); - Menu calculate = new Menu(); - MenuItem inputText = new MenuItem(); - Menu helpMenu = new Menu(); - MenuItem documentation = new MenuItem(); - MenuItem about = new MenuItem(); - protected CheckboxMenuItem seqLimits = new CheckboxMenuItem(); - Panel embeddedMenu; - Label embeddedEdit; - Label embeddedSearch; - Label embeddedView; - Label embeddedColour; - Label embeddedFile; - Label embeddedHelp; - Label embeddedCalculate; - FlowLayout flowLayout1; - - private void jbInit() throws Exception { - - setMenuBar(alignFrameMenuBar); - - MenuItem item; - - // dynamically fill save as menu with available formats - for (int i = 0; i < jalview.io.AppletFormatAdapter.WRITEABLE_FORMATS.length; i++) - { - - item = new MenuItem( jalview.io.AppletFormatAdapter.WRITEABLE_FORMATS[i]); - - item.addActionListener(new java.awt.event.ActionListener() - { - public void actionPerformed(ActionEvent e) - { - outputText_actionPerformed(e); - } - }); - - outputTextboxMenu.add(item); - } - closeMenuItem.addActionListener(this); - loadApplication.addActionListener(this); - - loadTree.addActionListener(this); - selectAllSequenceMenuItem.addActionListener(this); - deselectAllSequenceMenuItem.addActionListener(this); - invertSequenceMenuItem.addActionListener(this); - remove2LeftMenuItem.setLabel("Remove Left"); - remove2LeftMenuItem.addActionListener(this); - remove2RightMenuItem.setLabel("Remove Right"); - remove2RightMenuItem.addActionListener(this); - removeGappedColumnMenuItem.setLabel("Remove Empty Columns"); - removeGappedColumnMenuItem.addActionListener(this); - removeAllGapsMenuItem.setLabel("Remove All Gaps"); - removeAllGapsMenuItem.addActionListener(this); - viewBoxesMenuItem.setLabel("Boxes"); - viewBoxesMenuItem.setState(true); - viewBoxesMenuItem.addItemListener(this); - viewTextMenuItem.setLabel("Text"); - viewTextMenuItem.setState(true); - viewTextMenuItem.addItemListener(this); - sortPairwiseMenuItem.setLabel("by Pairwise Identity"); - sortPairwiseMenuItem.addActionListener(this); - sortIDMenuItem.setLabel("by ID"); - sortIDMenuItem.addActionListener(this); - sortGroupMenuItem.setLabel("by Group"); - sortGroupMenuItem.addActionListener(this); - removeRedundancyMenuItem.setLabel("Remove Redundancy..."); - removeRedundancyMenuItem.addActionListener(this); - pairwiseAlignmentMenuItem.setLabel("Pairwise Alignments..."); - pairwiseAlignmentMenuItem.addActionListener(this); - PCAMenuItem.setLabel("Principal Component Analysis"); - PCAMenuItem.addActionListener(this); - averageDistanceTreeMenuItem.setLabel( - "Average Distance Using % Identity"); - averageDistanceTreeMenuItem.addActionListener(this); - neighbourTreeMenuItem.setLabel("Neighbour Joining Using % Identity"); - neighbourTreeMenuItem.addActionListener(this); - alignFrameMenuBar.setFont(new java.awt.Font("Verdana", 0, 11)); - statusBar.setBackground(Color.white); - statusBar.setFont(new java.awt.Font("Verdana", 0, 11)); - statusBar.setText("Status bar"); - outputTextboxMenu.setLabel("Output to Textbox"); - clustalColour.setLabel("Clustalx"); - - clustalColour.addActionListener(this); - zappoColour.setLabel("Zappo"); - zappoColour.addActionListener(this); - taylorColour.setLabel("Taylor"); - taylorColour.addActionListener(this); - hydrophobicityColour.setLabel("Hydrophobicity"); - hydrophobicityColour.addActionListener(this); - helixColour.setLabel("Helix Propensity"); - helixColour.addActionListener(this); - strandColour.setLabel("Strand Propensity"); - strandColour.addActionListener(this); - turnColour.setLabel("Turn Propensity"); - turnColour.addActionListener(this); - buriedColour.setLabel("Buried Index"); - buriedColour.addActionListener(this); - userDefinedColour.setLabel("User Defined..."); - userDefinedColour.addActionListener(this); - PIDColour.setLabel("Percentage Identity"); - PIDColour.addActionListener(this); - BLOSUM62Colour.setLabel("BLOSUM62 Score"); - BLOSUM62Colour.addActionListener(this); - avDistanceTreeBlosumMenuItem.setLabel( - "Average Distance Using BLOSUM62"); - avDistanceTreeBlosumMenuItem.addActionListener(this); - njTreeBlosumMenuItem.setLabel("Neighbour Joining Using BLOSUM62"); - njTreeBlosumMenuItem.addActionListener(this); - annotationPanelMenuItem.setLabel("Show Annotations"); - annotationPanelMenuItem.addItemListener(this); - colourTextMenuItem.setLabel("Colour Text"); - colourTextMenuItem.addItemListener(this); - overviewMenuItem.setLabel("Overview Window"); - overviewMenuItem.addActionListener(this); - undoMenuItem.setEnabled(false); - undoMenuItem.setLabel("Undo"); - undoMenuItem.addActionListener(this); - redoMenuItem.setEnabled(false); - redoMenuItem.setLabel("Redo"); - redoMenuItem.addActionListener(this); - conservationMenuItem.setLabel("by Conservation"); - conservationMenuItem.addItemListener(this); - noColourmenuItem.setLabel("None"); - noColourmenuItem.addActionListener(this); - wrapMenuItem.setLabel("Wrap"); - wrapMenuItem.addItemListener(this); - renderGapsMenuItem.setLabel("Show Gaps"); - renderGapsMenuItem.setState(true); - renderGapsMenuItem.addItemListener(this); - findMenuItem.setLabel("Find..."); - findMenuItem.addActionListener(this); - searchMenu.setLabel("Search"); - - abovePIDThreshold.setLabel("Above Identity Threshold"); - abovePIDThreshold.addItemListener(this); - nucleotideColour.setLabel("Nucleotide"); - nucleotideColour.addActionListener(this); - deleteGroups.setLabel("Undefine Groups"); - deleteGroups.addActionListener(this); - copy.setLabel("Copy"); - copy.addActionListener(this); - cut.setLabel("Cut"); - cut.addActionListener(this); - delete.setLabel("Delete"); - delete.addActionListener(this); - pasteMenu.setLabel("Paste"); - pasteNew.setLabel("To New Alignment"); - pasteNew.addActionListener(this); - pasteThis.setLabel("Add To This Alignment"); - pasteThis.addActionListener(this); - applyToAllGroups.setLabel("Apply Colour To All Groups"); - applyToAllGroups.setState(true); - applyToAllGroups.addItemListener(this); - font.setLabel("Font..."); - font.addActionListener(this); - scaleAbove.setLabel("Scale Above"); - scaleAbove.setState(true); - scaleAbove.setEnabled(false); - scaleAbove.addItemListener(this); - scaleLeft.setEnabled(false); - scaleLeft.setState(true); - scaleLeft.setLabel("Scale Left"); - scaleLeft.addItemListener(this); - scaleRight.setEnabled(false); - scaleRight.setState(true); - scaleRight.setLabel("Scale Right"); - scaleRight.addItemListener(this); - modifyPID.setLabel("Modify Identity Threshold..."); - modifyPID.addActionListener(this); - modifyConservation.setLabel("Modify Conservation Threshold..."); - modifyConservation.addActionListener(this); - sortByTreeMenu.setLabel("By Tree Order"); - sort.setLabel("Sort"); - calculate.setLabel("Calculate Tree"); - autoCalculate.addItemListener(this); - inputText.setLabel("Input from textbox"); - inputText.addActionListener(this); - - helpMenu.setLabel("Help"); - documentation.setLabel("Documentation"); - documentation.addActionListener(this); - - about.setLabel("About..."); - about.addActionListener(this); - seqLimits.setState(true); - seqLimits.setLabel("Show Sequence Limits"); - seqLimits.addItemListener(this); - featureSettings.setLabel("Feature Settings..."); - featureSettings.addActionListener(this); - sequenceFeatures.setLabel("Sequence Features"); - sequenceFeatures.addItemListener(this); - sequenceFeatures.setState(false); - annotationColour.setLabel("by Annotation..."); - annotationColour.addActionListener(this); - invertSequenceMenuItem.setLabel("Invert Sequence Selection"); - invertColSel.setLabel("Invert Column Selection"); - menu1.setLabel("Show"); - showColumns.setLabel("All Columns "); - showSeqs.setLabel("All Sequences"); - menu2.setLabel("Hide"); - hideColumns.setLabel("Selected Columns"); - hideSequences.setLabel("Selected Sequences"); - invertColSel.addActionListener(this); - showColumns.addActionListener(this); - showSeqs.addActionListener(this); - hideColumns.addActionListener(this); - hideSequences.addActionListener(this); - - - alignFrameMenuBar.add(fileMenu); - alignFrameMenuBar.add(editMenu); - alignFrameMenuBar.add(searchMenu); - alignFrameMenuBar.add(viewMenu); - alignFrameMenuBar.add(colourMenu); - alignFrameMenuBar.add(calculateMenu); - alignFrameMenuBar.add(helpMenu); - fileMenu.add(inputText); - fileMenu.add(outputTextboxMenu); - if(jalviewServletURL!=null) - fileMenu.add(loadApplication); - fileMenu.addSeparator(); - fileMenu.add(loadTree); - fileMenu.add(closeMenuItem); - editMenu.add(undoMenuItem); - editMenu.add(redoMenuItem); - editMenu.add(cut); - editMenu.add(copy); - editMenu.add(pasteMenu); - editMenu.add(delete); - editMenu.addSeparator(); - editMenu.add(selectAllSequenceMenuItem); - editMenu.add(deselectAllSequenceMenuItem); - editMenu.add(invertSequenceMenuItem); - editMenu.add(invertColSel); - editMenu.add(deleteGroups); - editMenu.addSeparator(); - editMenu.add(remove2LeftMenuItem); - editMenu.add(remove2RightMenuItem); - editMenu.add(removeGappedColumnMenuItem); - editMenu.add(removeAllGapsMenuItem); - editMenu.add(removeRedundancyMenuItem); - searchMenu.add(findMenuItem); - viewMenu.add(font); - viewMenu.addSeparator(); - viewMenu.add(menu1); - viewMenu.add(menu2); - viewMenu.addSeparator(); - viewMenu.add(wrapMenuItem); - viewMenu.add(scaleAbove); - viewMenu.add(scaleLeft); - viewMenu.add(scaleRight); - viewMenu.addSeparator(); - viewMenu.add(seqLimits); - viewMenu.add(viewBoxesMenuItem); - viewMenu.add(viewTextMenuItem); - viewMenu.add(colourTextMenuItem); - viewMenu.add(renderGapsMenuItem); - viewMenu.add(annotationPanelMenuItem); - viewMenu.addSeparator(); - viewMenu.add(sequenceFeatures); - viewMenu.add(featureSettings); - viewMenu.addSeparator(); - viewMenu.add(overviewMenuItem); - colourMenu.add(applyToAllGroups); - colourMenu.addSeparator(); - colourMenu.add(noColourmenuItem); - colourMenu.add(clustalColour); - colourMenu.add(BLOSUM62Colour); - colourMenu.add(PIDColour); - colourMenu.add(zappoColour); - colourMenu.add(taylorColour); - colourMenu.add(hydrophobicityColour); - colourMenu.add(helixColour); - colourMenu.add(strandColour); - colourMenu.add(turnColour); - colourMenu.add(buriedColour); - colourMenu.add(nucleotideColour); - colourMenu.add(userDefinedColour); - colourMenu.addSeparator(); - colourMenu.add(conservationMenuItem); - colourMenu.add(modifyConservation); - colourMenu.add(abovePIDThreshold); - colourMenu.add(modifyPID); - colourMenu.add(annotationColour); - calculateMenu.add(sort); - calculateMenu.add(calculate); - calculateMenu.addSeparator(); - calculateMenu.add(pairwiseAlignmentMenuItem); - calculateMenu.add(PCAMenuItem); - calculateMenu.add(autoCalculate); - this.add(statusBar, BorderLayout.SOUTH); - pasteMenu.add(pasteNew); - pasteMenu.add(pasteThis); - sort.add(sortIDMenuItem); - sort.add(sortByTreeMenu); - sort.add(sortGroupMenuItem); - sort.add(sortPairwiseMenuItem); - calculate.add(averageDistanceTreeMenuItem); - calculate.add(neighbourTreeMenuItem); - calculate.add(avDistanceTreeBlosumMenuItem); - calculate.add(njTreeBlosumMenuItem); - helpMenu.add(documentation); - helpMenu.add(about); - menu1.add(showColumns); - menu1.add(showSeqs); - menu2.add(hideColumns); - menu2.add(hideSequences); - } - - public void setEmbedded() - { - - embeddedMenu = new Panel(); - embeddedEdit = new Label(); - embeddedSearch = new Label(); - embeddedView = new Label(); - embeddedColour = new Label(); - embeddedFile = new Label(); - embeddedHelp = new Label(); - embeddedCalculate = new Label(); - flowLayout1 = new FlowLayout(); - embeddedMenu.setBackground(Color.lightGray); - embeddedMenu.setLayout(flowLayout1); - embeddedEdit.setText("Edit"); - embeddedEdit.setFont(new java.awt.Font("Arial", Font.PLAIN, 10)); - embeddedSearch.setText("Search"); - embeddedSearch.setFont(new java.awt.Font("Arial", Font.PLAIN, 10)); - embeddedView.setText("View"); - embeddedView.setFont(new java.awt.Font("Arial", Font.PLAIN, 10)); - embeddedColour.setText("Colour"); - embeddedColour.setFont(new java.awt.Font("Arial", Font.PLAIN, 10)); - embeddedFile.setFont(new java.awt.Font("Arial", Font.PLAIN, 10)); - embeddedFile.setText("File"); - embeddedHelp.setFont(new java.awt.Font("Arial", Font.PLAIN, 10)); - embeddedHelp.setText("Help"); - embeddedCalculate.setFont(new java.awt.Font("Arial", Font.PLAIN, 10)); - embeddedCalculate.setText("Calculate"); - embeddedMenu.add(embeddedFile); - embeddedMenu.add(embeddedEdit); - embeddedMenu.add(embeddedSearch); - embeddedMenu.add(embeddedView); - embeddedMenu.add(embeddedColour); - embeddedMenu.add(embeddedCalculate); - embeddedMenu.add(embeddedHelp); - flowLayout1.setAlignment(FlowLayout.LEFT); - flowLayout1.setHgap(2); - flowLayout1.setVgap(0); - embeddedFile.addMouseListener(this); - embeddedEdit.addMouseListener(this); - embeddedSearch.addMouseListener(this); - embeddedView.addMouseListener(this); - embeddedColour.addMouseListener(this); - embeddedCalculate.addMouseListener(this); - embeddedHelp.addMouseListener(this); - - // setVisible(false); - fileMenu.remove(closeMenuItem); - fileMenu.remove(3); // Seperator + new MCview.AppletPDBViewer(pdb, seqs, chains, alignPanel, protocol); + } - viewport.applet.setLayout(new BorderLayout()); - viewport.applet.add(embeddedMenu, BorderLayout.NORTH); - viewport.applet.add(statusBar, BorderLayout.SOUTH); - // viewport.applet.validate(); + } - alignPanel.setSize(viewport.applet.size().width, viewport.applet.size().height - - embeddedMenu.HEIGHT - statusBar.HEIGHT); + public void alignedStructureView(JalviewLite applet, PDBEntry[] pdb, + SequenceI[][] seqs, String[][] chains, String[] protocols) + { + // TODO Auto-generated method stub + System.err.println("Aligned Structure View: Not yet implemented."); + } - viewport.applet.add(alignPanel, BorderLayout.CENTER); - viewport.applet.validate(); + /** + * modify the current selection, providing the user has not made a selection + * already. + * + * @param sel + * - sequences from this alignment + * @param csel + * - columns to be selected on the alignment + */ + public void select(SequenceGroup sel, ColumnSelection csel) + { + alignPanel.seqPanel.selection(sel, csel, null); + } + public void scrollTo(int row, int column) + { + alignPanel.seqPanel.scrollTo(row, column); } + public void scrollToRow(int row) + { + alignPanel.seqPanel.scrollToRow(row); + } + public void scrollToColumn(int column) + { + alignPanel.seqPanel.scrollToColumn(column); + } - PopupMenu filePopup, editPopup, searchPopup, - viewPopup, colourPopup, calculatePopup, helpPopup; - MenuItem featureSettings = new MenuItem(); - CheckboxMenuItem sequenceFeatures = new CheckboxMenuItem(); - MenuItem annotationColour = new MenuItem(); - MenuItem invertColSel = new MenuItem(); - Menu menu1 = new Menu(); - MenuItem showColumns = new MenuItem(); - MenuItem showSeqs = new MenuItem(); - Menu menu2 = new Menu(); - MenuItem hideColumns = new MenuItem(); - MenuItem hideSequences = new MenuItem(); + /** + * @return the alignments unique ID. + */ + public String getSequenceSetId() + { + return viewport.getSequenceSetId(); + } - public void mousePressed(MouseEvent evt) + /** + * Load the (T-Coffee) score file from the specified url + * + * @param source + * File/URL/T-COFFEE score file contents + * @throws IOException + * @return true if alignment was annotated with data from source + */ + public boolean loadScoreFile(String source) throws IOException { - PopupMenu popup = null; - Label source = (Label)evt.getSource(); - if(source==embeddedFile) - { - popup = filePopup = genPopupMenu(filePopup, fileMenu); - } - else if(source==embeddedEdit) - { - popup = editPopup = genPopupMenu(editPopup, editMenu); - } - else if(source==embeddedSearch) - { - popup = searchPopup = genPopupMenu(searchPopup, searchMenu); - } - else if(source==embeddedView) + + TCoffeeScoreFile file = new TCoffeeScoreFile(source, + AppletFormatAdapter.checkProtocol(source)); + if (!file.isValid()) { - popup = viewPopup = genPopupMenu(viewPopup, viewMenu); + // TODO: raise dialog for gui + System.err.println("Problems parsing T-Coffee scores: " + + file.getWarningMessage()); + System.err.println("Origin was:\n" + source); + return false; } - else if(source==embeddedColour) + + /* + * check that the score matrix matches the alignment dimensions + */ + AlignmentI aln; + if ((aln = viewport.getAlignment()) != null + && (aln.getHeight() != file.getHeight() || aln.getWidth() != file + .getWidth())) { - popup = colourPopup = genPopupMenu(colourPopup, colourMenu); + // TODO: raise a dialog box here rather than bomb out. + System.err + .println("The scores matrix does not match the alignment dimensions"); + } - else if(source==embeddedCalculate) + + // TODO add parameter to indicate if matching should be done + if (file.annotateAlignment(alignPanel.getAlignment(), false)) { - popup = calculatePopup = genPopupMenu(calculatePopup, calculateMenu); + alignPanel.fontChanged(); + tcoffeeColour.setEnabled(true); + // switch to this color + changeColour(new TCoffeeColourScheme(alignPanel.getAlignment())); + return true; } - else if(source==embeddedHelp) + else { - popup = helpPopup = genPopupMenu(helpPopup, helpMenu); + System.err.println("Problems resolving T-Coffee scores:"); + if (file.getWarningMessage() != null) + { + System.err.println(file.getWarningMessage()); + } } + return false; + } - embeddedMenu.add(popup); - popup.show(embeddedMenu, - source.getBounds().x, - source.getBounds().y + source.getBounds().getSize().height); + public SplitFrame getSplitFrame() + { + return this.splitFrame; } - PopupMenu genPopupMenu(PopupMenu popup, Menu original) + public void setSplitFrame(SplitFrame sf) { - if(popup!=null) - { - return popup; - } - popup = new PopupMenu(); - int m, mSize = original.getItemCount(); - for(m=0; m