X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FAlignFrame.java;h=700c2293a736a45c82b5c53937d6b80600e846c2;hb=b57a02c25e335d033c97f8a6bacd6b54f62bd2b6;hp=a07634564e05f79a67ea56fd1b92c4cdc74a275d;hpb=7bc226b58110fa26d9dbd3f0c78095d06909ffc3;p=jalview.git diff --git a/src/jalview/appletgui/AlignFrame.java b/src/jalview/appletgui/AlignFrame.java old mode 100755 new mode 100644 index a076345..700c229 --- a/src/jalview/appletgui/AlignFrame.java +++ b/src/jalview/appletgui/AlignFrame.java @@ -1,54 +1,113 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer - * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7) + * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle * - * This program is free software; you can redistribute it and/or + * 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 2 - * of the License, or (at your option) any later version. + * 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 + * You should have received a copy of the GNU General Public License along with Jalview. If not, see . */ - package jalview.appletgui; -import java.io.*; -import java.net.*; -import java.util.*; - -import java.awt.*; -import java.awt.event.*; - -import jalview.analysis.*; -import jalview.commands.*; -import jalview.datamodel.*; -import jalview.io.*; -import jalview.schemes.*; - -public class AlignFrame - extends Frame implements ActionListener, - ItemListener, KeyListener, MouseListener +import jalview.analysis.AAFrequency; +import jalview.analysis.AlignmentSorter; +import jalview.analysis.Conservation; +import jalview.api.SequenceStructureBinding; +import jalview.bin.JalviewLite; +import jalview.commands.CommandI; +import jalview.commands.EditCommand; +import jalview.commands.OrderCommand; +import jalview.commands.RemoveGapColCommand; +import jalview.commands.RemoveGapsCommand; +import jalview.commands.SlideSequencesCommand; +import jalview.commands.TrimRegionCommand; +import jalview.datamodel.Alignment; +import jalview.datamodel.AlignmentI; +import jalview.datamodel.AlignmentOrder; +import jalview.datamodel.ColumnSelection; +import jalview.datamodel.PDBEntry; +import jalview.datamodel.Sequence; +import jalview.datamodel.SequenceCollectionI; +import jalview.datamodel.SequenceGroup; +import jalview.datamodel.SequenceI; +import jalview.io.AnnotationFile; +import jalview.io.AppletFormatAdapter; +import jalview.io.FeaturesFile; +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.RNAHelicesColourChooser; +import jalview.schemes.ResidueProperties; +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 java.awt.BorderLayout; +import java.awt.Canvas; +import java.awt.CheckboxMenuItem; +import java.awt.Color; +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.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.io.InputStreamReader; +import java.net.URL; +import java.net.URLEncoder; +import java.util.Enumeration; +import java.util.Hashtable; +import java.util.List; +import java.util.StringTokenizer; +import java.util.Vector; + +public class AlignFrame extends EmbmenuFrame implements ActionListener, + ItemListener, KeyListener { public AlignmentPanel alignPanel; + public AlignViewport viewport; + int DEFAULT_WIDTH = 700; + int DEFAULT_HEIGHT = 500; String jalviewServletURL; - public AlignFrame(AlignmentI al, - jalview.bin.JalviewLite applet, - String title, - boolean embedded) + public AlignFrame(AlignmentI al, jalview.bin.JalviewLite applet, + String title, boolean embedded) { - if (applet != null) { jalviewServletURL = applet.getParameter("APPLICATION_URL"); @@ -57,8 +116,7 @@ public class AlignFrame try { jbInit(); - } - catch (Exception ex) + } catch (Exception ex) { ex.printStackTrace(); } @@ -70,6 +128,13 @@ public class AlignFrame viewport.updateConsensus(alignPanel); annotationPanelMenuItem.setState(viewport.showAnnotation); + displayNonconservedMenuItem.setState(viewport.getShowUnconserved()); + followMouseOverFlag.setState(viewport.getFollowHighlight()); + showGroupConsensus.setState(viewport.isShowGroupConsensus()); + showGroupConservation.setState(viewport.isShowGroupConservation()); + showConsensusHistogram.setState(viewport.isShowConsensusHistogram()); + showSequenceLogo.setState(viewport.isShowSequenceLogo()); + normSequenceLogo.setState(viewport.isNormaliseSequenceLogo()); seqLimits.setState(viewport.showJVSuffix); @@ -86,6 +151,10 @@ public class AlignFrame { sortPairwiseMenuItem_actionPerformed(); } + else if (param.equalsIgnoreCase("Length")) + { + sortLengthMenuItem_actionPerformed(); + } } param = applet.getParameter("wrap"); @@ -97,7 +166,12 @@ public class AlignFrame wrapMenuItem_actionPerformed(); } } - + param = applet.getParameter("centrecolumnlabels"); + if (param != null) + { + centreColumnLabelFlag.setState(true); + centreColumnLabelFlag_stateChanged(); + } try { param = applet.getParameter("windowWidth"); @@ -112,32 +186,44 @@ public class AlignFrame int height = Integer.parseInt(param); DEFAULT_HEIGHT = height; } + } catch (Exception ex) + { } - 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 + if (viewport.getAlignment().isNucleotide()) + { + viewport.updateStrucConsensus(alignPanel); + if (viewport.getAlignment().hasRNAStructure()) + { + RNAHelixColour.setEnabled(true); + } + else + { + RNAHelixColour.setEnabled(false); + } + } + else + { + RNAHelixColour.setEnabled(false); + purinePyrimidineColour.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); + createAlignFrameWindow(embedded, title); - if (embedded) - { - setEmbedded(); - } - else - { - add(alignPanel, BorderLayout.CENTER); - jalview.bin.JalviewLite.addFrame(this, title, DEFAULT_WIDTH, - DEFAULT_HEIGHT); - } - alignPanel.validate(); - alignPanel.repaint(); + validate(); + alignPanel.adjustAnnotationHeight(); + alignPanel.paintAlignment(true); } public AlignViewport getAlignViewport() @@ -151,25 +237,47 @@ public class AlignFrame } /** - * 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, String type) + { + return parseFeaturesFile(file, type, true); + } + + /** + * 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 + * @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, String type, + boolean autoenabledisplay) { + // TODO: test if importing a features file onto an alignment which already + // has features with links overwrites the original links. + 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) + featuresFile = new jalview.io.FeaturesFile(file, type) + .parse(viewport.getAlignment(), alignPanel.seqPanel.seqCanvas + .getFeatureRenderer().featureColours, featureLinks, + true, viewport.applet.getDefaultParameter( + "relaxedidmatch", false)); + } catch (Exception ex) { ex.printStackTrace(); } @@ -178,316 +286,370 @@ public class AlignFrame { if (featureLinks.size() > 0) { - alignPanel.seqPanel.seqCanvas - .getFeatureRenderer().featureLinks = featureLinks; + alignPanel.seqPanel.seqCanvas.getFeatureRenderer().featureLinks = featureLinks; + } + if (autoenabledisplay) + { + viewport.showSequenceFeatures = true; + sequenceFeatures.setState(true); + } + if (viewport.featureSettings != null) + { + viewport.featureSettings.refreshTable(); } - viewport.showSequenceFeatures = true; - sequenceFeatures.setState(true); - alignPanel.repaint(); + alignPanel.paintAlignment(true); + statusBar.setText("Successfully added features to alignment."); } - + return featuresFile; } + @Override public void keyPressed(KeyEvent evt) { 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()) - { - 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 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() - || evt.isShiftDown() - || evt.isAltDown() - ); - } - 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() - || evt.isShiftDown() - || evt.isAltDown()); - } - 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_ENTER: - case KeyEvent.VK_COMMA: - if (viewport.cursorMode) - { - alignPanel.seqPanel.setCursorRowAndColumn(); - } - 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_Q: - if (viewport.cursorMode) - { - alignPanel.seqPanel.setSelectionAreaAtCursor(true); - } - break; - case KeyEvent.VK_M: - if (viewport.cursorMode) - { - alignPanel.seqPanel.setSelectionAreaAtCursor(false); - } - 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_F2: - viewport.cursorMode = !viewport.cursorMode; - statusBar.setText("Keyboard editing mode is " + - (viewport.cursorMode ? "on" : "off")); - if (viewport.cursorMode) - { - alignPanel.seqPanel.seqCanvas.cursorX = viewport.startRes; - alignPanel.seqPanel.seqCanvas.cursorY = viewport.startSeq; - } - break; + case KeyEvent.VK_ENTER: + case KeyEvent.VK_COMMA: + if (viewport.cursorMode) + { + alignPanel.seqPanel.setCursorRowAndColumn(); + } + break; - case KeyEvent.VK_F: - if (evt.isControlDown()) - { - findMenuItem_actionPerformed(); - } - 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_H: + case KeyEvent.VK_F2: + viewport.cursorMode = !viewport.cursorMode; + statusBar.setText("Keyboard editing mode is " + + (viewport.cursorMode ? "on" : "off")); + if (viewport.cursorMode) { - boolean toggleSeqs = !evt.isControlDown(); - boolean toggleCols = !evt.isShiftDown(); - boolean hide = false; - SequenceGroup sg = viewport.getSelectionGroup(); + alignPanel.seqPanel.seqCanvas.cursorX = viewport.startRes; + alignPanel.seqPanel.seqCanvas.cursorY = viewport.startSeq; + } + break; - if (toggleSeqs) - { - if (sg != null && sg.getSize() != viewport.alignment.getHeight()) - { - hide = true; - viewport.hideAllSelectedSeqs(); - } - else if (! (toggleCols && viewport.colSel.getSelected().size() > 0)) - { - viewport.showAllHiddenSeqs(); - } - } + case KeyEvent.VK_F: + if (evt.isControlDown()) + { + findMenuItem_actionPerformed(); + } + break; - if (toggleCols) - { - if (viewport.colSel.getSelected().size() > 0) - { - viewport.hideSelectedColumns(); - if (!toggleSeqs) - { - viewport.selectionGroup = sg; - } - } - else if (!hide) - { - viewport.showAllHiddenColumns(); - } - } - break; + case KeyEvent.VK_H: + { + boolean toggleSeqs = !evt.isControlDown(); + boolean toggleCols = !evt.isShiftDown(); + toggleHiddenRegions(toggleSeqs, toggleCols); + break; + } + + case KeyEvent.VK_PAGE_UP: + if (viewport.wrapAlignment) + { + alignPanel.scrollUp(true); + } + else + { + alignPanel.setScrollValues(viewport.startRes, viewport.startSeq + - viewport.endSeq + viewport.startSeq); + } + break; + + case KeyEvent.VK_PAGE_DOWN: + if (viewport.wrapAlignment) + { + alignPanel.scrollUp(false); + } + else + { + alignPanel.setScrollValues(viewport.startRes, viewport.startSeq + + viewport.endSeq - viewport.startSeq); } + break; - case KeyEvent.VK_PAGE_UP: - if (viewport.wrapAlignment) + 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.scrollUp(true); + this.removeAllGapsMenuItem_actionPerformed(); } else { - alignPanel.setScrollValues(viewport.startRes, - viewport.startSeq - - viewport.endSeq + viewport.startSeq); + removeGappedColumnMenuItem_actionPerformed(); } - break; - - case KeyEvent.VK_PAGE_DOWN: - if (viewport.wrapAlignment) + } + break; + case KeyEvent.VK_I: + if (evt.isControlDown()) + { + if (evt.isAltDown()) { - alignPanel.scrollUp(false); + invertColSel_actionPerformed(); } else { - alignPanel.setScrollValues(viewport.startRes, - viewport.startSeq - + viewport.endSeq - viewport.startSeq); + invertSequenceMenuItem_actionPerformed(); } - break; + } + break; - case KeyEvent.VK_Z: - if (evt.isControlDown()) - { - undoMenuItem_actionPerformed(); - } - break; + case KeyEvent.VK_U: + if (evt.isControlDown()) + { + this.deleteGroups_actionPerformed(); + } + break; - case KeyEvent.VK_Y: - if (evt.isControlDown()) - { - redoMenuItem_actionPerformed(); - } - break; + case KeyEvent.VK_T: + if (evt.isControlDown()) + { + newView(null); + } + break; - case KeyEvent.VK_L: - if (evt.isControlDown()) - { - trimAlignment(true); - } - break; + } + alignPanel.paintAlignment(true); + } - case KeyEvent.VK_R: - if (evt.isControlDown()) + /** + * called by key handler and the hide all/show all menu items + * + * @param toggleSeqs + * @param toggleCols + */ + private void toggleHiddenRegions(boolean toggleSeqs, boolean toggleCols) + { + boolean hide = false; + SequenceGroup sg = viewport.getSelectionGroup(); + if (!toggleSeqs && !toggleCols) + { + // Hide everything by the current selection - this is a hack - we do the + // invert and then hide + // first check that there will be visible columns after the invert. + if ((viewport.getColumnSelection() != null + && viewport.getColumnSelection().getSelected() != null && viewport + .getColumnSelection().getSelected().size() > 0) + || (sg != null && sg.getSize() > 0 && sg.getStartRes() <= sg + .getEndRes())) + { + // now invert the sequence set, if required - empty selection implies + // that no hiding is required. + if (sg != null) { - trimAlignment(false); - } - break; + invertSequenceMenuItem_actionPerformed(); + sg = viewport.getSelectionGroup(); + toggleSeqs = true; - case KeyEvent.VK_E: - if (evt.isControlDown()) - { - if (evt.isShiftDown()) - { - this.removeAllGapsMenuItem_actionPerformed(); - } - else - { - removeGappedColumnMenuItem_actionPerformed(); - } - } - break; - case KeyEvent.VK_I: - if (evt.isControlDown()) - { - if (evt.isAltDown()) - { - viewport.invertColumnSelection(); - } - else - { - this.invertSequenceMenuItem_actionPerformed(); - } } - break; + 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; + } + } - case KeyEvent.VK_U: - if (evt.isControlDown()) - { - this.deleteGroups_actionPerformed(); - } - break; + if (toggleSeqs) + { + if (sg != null && sg.getSize() != viewport.getAlignment().getHeight()) + { + hide = true; + viewport.hideAllSelectedSeqs(); + } + else if (!(toggleCols && viewport.getColumnSelection().getSelected() + .size() > 0)) + { + viewport.showAllHiddenSeqs(); + } + } - case KeyEvent.VK_T: - if (evt.isControlDown()) + if (toggleCols) + { + if (viewport.getColumnSelection().getSelected().size() > 0) + { + viewport.hideSelectedColumns(); + if (!toggleSeqs) { - newView(); + viewport.setSelectionGroup(sg); } - break; - + } + else if (!hide) + { + viewport.showAllHiddenColumns(); + } } - alignPanel.repaint(); } + @Override public void keyReleased(KeyEvent evt) - {} + { + } + @Override public void keyTyped(KeyEvent evt) - {} + { + } + @Override public void itemStateChanged(ItemEvent evt) { - if (evt.getSource() == colourTextMenuItem) + if (evt.getSource() == displayNonconservedMenuItem) + { + displayNonconservedMenuItem_actionPerformed(); + } + else if (evt.getSource() == colourTextMenuItem) { colourTextMenuItem_actionPerformed(); } @@ -547,12 +709,61 @@ public class AlignFrame } else if (evt.getSource() == autoCalculate) { - viewport.autocalculateConsensus = autoCalculate.getState(); + viewport.autoCalculateConsensus = autoCalculate.getState(); + } + else if (evt.getSource() == sortByTree) + { + viewport.sortByTree = sortByTree.getState(); } + else if (evt.getSource() == this.centreColumnLabelFlag) + { + centreColumnLabelFlag_stateChanged(); + } + else if (evt.getSource() == this.followMouseOverFlag) + { + mouseOverFlag_stateChanged(); + } + else if (evt.getSource() == showGroupConsensus) + { + showGroupConsensus_actionPerformed(); + } + else if (evt.getSource() == showGroupConservation) + { + showGroupConservation_actionPerformed(); + } + else if (evt.getSource() == showSequenceLogo) + { + showSequenceLogo_actionPerformed(); + } + else if (evt.getSource() == normSequenceLogo) + { + normSequenceLogo_actionPerformed(); + } + else if (evt.getSource() == showConsensusHistogram) + { + showConsensusHistogram_actionPerformed(); + } + else if (evt.getSource() == applyAutoAnnotationSettings) + { + applyAutoAnnotationSettings_actionPerformed(); + } + alignPanel.paintAlignment(true); + } - alignPanel.repaint(); + private void mouseOverFlag_stateChanged() + { + viewport.followHighlight = 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) { Object source = evt.getSource(); @@ -633,6 +844,10 @@ public class AlignFrame { delete_actionPerformed(); } + else if (source == grpsFromSelection) + { + makeGrpsFromSelection_actionPerformed(); + } else if (source == deleteGroups) { deleteGroups_actionPerformed(); @@ -652,7 +867,7 @@ public class AlignFrame else if (source == invertColSel) { viewport.invertColumnSelection(); - alignPanel.repaint(); + alignPanel.paintAlignment(true); } else if (source == remove2LeftMenuItem) { @@ -674,36 +889,93 @@ public class AlignFrame { findMenuItem_actionPerformed(); } - else if (source == font) + else if (source == font) + { + new FontChooser(alignPanel); + } + else if (source == newView) + { + newView(null); + } + else if (source == showColumns) + { + viewport.showAllHiddenColumns(); + alignPanel.paintAlignment(true); + } + else if (source == showSeqs) + { + viewport.showAllHiddenSeqs(); + alignPanel.paintAlignment(true); + } + else if (source == hideColumns) + { + viewport.hideSelectedColumns(); + alignPanel.paintAlignment(true); + } + else if (source == hideSequences + && viewport.getSelectionGroup() != null) + { + viewport.hideAllSelectedSeqs(); + alignPanel.paintAlignment(true); + } + else if (source == hideAllButSelection) + { + toggleHiddenRegions(false, false); + alignPanel.paintAlignment(true); + } + else if (source == hideAllSelection) + { + SequenceGroup sg = viewport.getSelectionGroup(); + viewport.expandColSelection(sg, false); + viewport.hideAllSelectedSeqs(); + viewport.hideSelectedColumns(); + alignPanel.paintAlignment(true); + } + else if (source == showAllHidden) + { + viewport.showAllHiddenColumns(); + viewport.showAllHiddenSeqs(); + alignPanel.paintAlignment(true); + } + else if (source == showGroupConsensus) { - new FontChooser(alignPanel); + showGroupConsensus_actionPerformed(); } - else if (source == newView) + else if (source == showGroupConservation) { - newView(); + showGroupConservation_actionPerformed(); } - else if (source == showColumns) + else if (source == showSequenceLogo) { - viewport.showAllHiddenColumns(); - alignPanel.repaint(); + showSequenceLogo_actionPerformed(); } - else if (source == showSeqs) + else if (source == normSequenceLogo) { - viewport.showAllHiddenSeqs(); + normSequenceLogo_actionPerformed(); } - else if (source == hideColumns) + else if (source == showConsensusHistogram) { - viewport.hideSelectedColumns(); - alignPanel.repaint(); + showConsensusHistogram_actionPerformed(); } - else if (source == hideSequences && viewport.getSelectionGroup() != null) + else if (source == applyAutoAnnotationSettings) { - viewport.hideAllSelectedSeqs(); + 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, "Alignment Properties: " + + getTitle(), 400, 250); + } else if (source == overviewMenuItem) { overviewMenuItem_actionPerformed(); @@ -715,8 +987,7 @@ public class AlignFrame else if (source == clustalColour) { abovePIDThreshold.setState(false); - changeColour(new ClustalxColourScheme(viewport.alignment.getSequences(), - viewport.alignment.getWidth())); + changeColour(new ClustalxColourScheme(viewport.getAlignment(), null)); } else if (source == zappoColour) { @@ -750,6 +1021,14 @@ public class AlignFrame { changeColour(new NucleotideColourScheme()); } + else if (source == purinePyrimidineColour) + { + changeColour(new PurinePyrimidineColourScheme()); + } + else if (source == RNAHelixColour) + { + new RNAHelicesColourChooser(viewport, alignPanel); + } else if (source == modifyPID) { modifyPID_actionPerformed(); @@ -770,6 +1049,10 @@ public class AlignFrame { changeColour(new Blosum62ColourScheme()); } + else if (source == tcoffeeColour) + { + changeColour(new TCoffeeColourScheme(alignPanel.getAlignment())); + } else if (source == annotationColour) { new AnnotationColourChooser(viewport, alignPanel); @@ -782,6 +1065,10 @@ public class AlignFrame { sortIDMenuItem_actionPerformed(); } + else if (source == sortLengthMenuItem) + { + sortLengthMenuItem_actionPerformed(); + } else if (source == sortGroupMenuItem) { sortGroupMenuItem_actionPerformed(); @@ -839,17 +1126,16 @@ public class AlignFrame 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(), - viewport.showJVSuffix)); + "Alignment output - " + e.getActionCommand(), 600, 500); + cap.setText(new AppletFormatAdapter().formatSequences( + e.getActionCommand(), viewport.getAlignment(), + viewport.showJVSuffix)); } public void loadAnnotations() { CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this); - cap.setText("Paste your features / annotations file here."); + cap.setText("Paste your features / annotations / T-coffee score file here."); cap.setAnnotationImport(); Frame frame = new Frame(); frame.add(cap); @@ -860,50 +1146,80 @@ public class AlignFrame public String outputAnnotations(boolean displayTextbox) { String annotation = new AnnotationFile().printAnnotations( - viewport.showAnnotation ? viewport.alignment.getAlignmentAnnotation() : null, - viewport.alignment.getGroups()); + viewport.showAnnotation ? viewport.getAlignment() + .getAlignmentAnnotation() : null, viewport + .getAlignment().getGroups(), ((Alignment) viewport + .getAlignment()).alignmentProperties); if (displayTextbox) { CutAndPasteTransfer cap = new CutAndPasteTransfer(false, this); Frame frame = new Frame(); frame.add(cap); - jalview.bin.JalviewLite.addFrame(frame, - "Annotations", - 600, 500); + jalview.bin.JalviewLite.addFrame(frame, "Annotations", 600, 500); cap.setText(annotation); } return annotation; } + private Hashtable getDisplayedFeatureCols() + { + if (alignPanel.getFeatureRenderer() != null + && viewport.featuresDisplayed != null) + { + FeatureRenderer fr = alignPanel.getFeatureRenderer(); + Hashtable fcols = new Hashtable(); + Enumeration en = viewport.featuresDisplayed.keys(); + while (en.hasMoreElements()) + { + Object col = en.nextElement(); + fcols.put(col, fr.featureColours.get(col)); + } + return fcols; + } + return null; + } + public String outputFeatures(boolean displayTextbox, String format) { String features; if (format.equalsIgnoreCase("Jalview")) { - features = new FeaturesFile().printJalviewFormat( - viewport.alignment.getSequencesArray(), - viewport.featuresDisplayed); + features = new FeaturesFile().printJalviewFormat(viewport + .getAlignment().getSequencesArray(), + getDisplayedFeatureCols()); } else { - features = new FeaturesFile().printGFFFormat( - viewport.alignment.getSequencesArray(), - viewport.featuresDisplayed); + features = new FeaturesFile().printGFFFormat(viewport.getAlignment() + .getSequencesArray(), getDisplayedFeatureCols()); } if (displayTextbox) { - CutAndPasteTransfer cap = new CutAndPasteTransfer(false, this); + 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, - "Features", - 600, 500); - + jalview.bin.JalviewLite.addFrame(frame, "Features", 600, 500); cap.setText(features); } + else + { + if (features == null) + features = ""; + } return features; } @@ -912,8 +1228,8 @@ public class AlignFrame { StringBuffer url = new StringBuffer(jalviewServletURL); - url.append("?open=" + - appendProtocol(viewport.applet.getParameter("file"))); + url.append("?open=" + + appendProtocol(viewport.applet.getParameter("file"))); if (viewport.applet.getParameter("features") != null) { @@ -935,17 +1251,26 @@ public class AlignFrame if (viewport.applet.getParameter("defaultColour") != null) { - url.append("&colour=" + - removeWhiteSpace(viewport.applet.getParameter("defaultColour")) - ); + url.append("&colour=" + + removeWhiteSpace(viewport.applet + .getParameter("defaultColour"))); } if (viewport.applet.getParameter("userDefinedColour") != null) { - url.append("&colour=" + - removeWhiteSpace(viewport.applet.getParameter( - "userDefinedColour")) - ); + 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"); @@ -974,7 +1299,15 @@ public class AlignFrame 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; @@ -985,19 +1318,30 @@ public class AlignFrame public void closeMenuItem_actionPerformed() { PaintRefresher.RemoveComponent(alignPanel); - PaintRefresher.RemoveComponent(alignPanel.seqPanel.seqCanvas); - PaintRefresher.RemoveComponent(alignPanel.idPanel.idCanvas); + 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(); } /** - * DOCUMENT ME! + * TODO: JAL-1104 */ void updateEditMenuBar() { @@ -1028,6 +1372,9 @@ public class AlignFrame } } + /** + * TODO: JAL-1104 + */ public void addHistoryItem(CommandI command) { if (command.getSize() > 0) @@ -1035,14 +1382,15 @@ public class AlignFrame viewport.historyList.push(command); viewport.redoList.removeAllElements(); updateEditMenuBar(); - viewport.hasHiddenColumns = viewport.colSel.getHiddenColumns() != null; + viewport.updateHiddenColumns(); } } /** - * DOCUMENT ME! - * - * @param e DOCUMENT ME! + * TODO: JAL-1104 DOCUMENT ME! + * + * @param e + * DOCUMENT ME! */ protected void undoMenuItem_actionPerformed() { @@ -1053,20 +1401,28 @@ public class AlignFrame CommandI command = (CommandI) viewport.historyList.pop(); viewport.redoList.push(command); - command.undoCommand(); + command.undoCommand(null); AlignViewport originalSource = getOriginatingSource(command); - - originalSource.hasHiddenColumns = viewport.colSel.getHiddenColumns() != null; + // 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.alignment.getSequences()); + originalSource.firePropertyChange("alignment", null, originalSource + .getAlignment().getSequences()); } /** - * DOCUMENT ME! - * - * @param e DOCUMENT ME! + * TODO: JAL-1104 DOCUMENT ME! + * + * @param e + * DOCUMENT ME! */ protected void redoMenuItem_actionPerformed() { @@ -1077,36 +1433,44 @@ public class AlignFrame CommandI command = (CommandI) viewport.redoList.pop(); viewport.historyList.push(command); - command.doCommand(); + command.doCommand(null); AlignViewport originalSource = getOriginatingSource(command); - originalSource.hasHiddenColumns = viewport.colSel.getHiddenColumns() != null; + // 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.alignment.getSequences()); + originalSource.firePropertyChange("alignment", null, originalSource + .getAlignment().getSequences()); } AlignViewport getOriginatingSource(CommandI command) { AlignViewport originalSource = null; - //For sequence removal and addition, we need to fire - //the property change event FROM the viewport where the - //original alignment was altered + // For sequence removal and addition, we need to fire + // the property change event FROM the viewport where the + // original alignment was altered AlignmentI al = null; if (command instanceof EditCommand) { EditCommand editCommand = (EditCommand) command; al = editCommand.getAlignment(); - Vector comps = (Vector) PaintRefresher.components - .get(viewport.getSequenceSetId()); + Vector comps = (Vector) PaintRefresher.components.get(viewport + .getSequenceSetId()); for (int i = 0; i < comps.size(); i++) { if (comps.elementAt(i) instanceof AlignmentPanel) { - if (al == ( (AlignmentPanel) comps.elementAt(i)).av.alignment) + if (al == ((AlignmentPanel) comps.elementAt(i)).av.getAlignment()) { - originalSource = ( (AlignmentPanel) comps.elementAt(i)).av; + originalSource = ((AlignmentPanel) comps.elementAt(i)).av; break; } } @@ -1115,11 +1479,11 @@ public class AlignFrame if (originalSource == null) { - //The original view is closed, we must validate - //the current view against the closed view first + // The original view is closed, we must validate + // the current view against the closed view first if (al != null) { - PaintRefresher.validateSequences(al, viewport.alignment); + PaintRefresher.validateSequences(al, viewport.getAlignment()); } originalSource = viewport; @@ -1135,53 +1499,98 @@ public class AlignFrame { return; } + viewport.getAlignment().moveSelectedSequencesByOne(sg, + up ? null : viewport.getHiddenRepSequences(), up); + 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 (up) + if (sg.size() < 1) { - for (int i = 1; i < viewport.alignment.getHeight(); i++) - { - SequenceI seq = viewport.alignment.getSequenceAt(i); - if (!sg.getSequences(null).contains(seq)) - { - continue; - } + return; + } - SequenceI temp = viewport.alignment.getSequenceAt(i - 1); - if (sg.getSequences(null).contains(temp)) - { - continue; - } + Vector invertGroup = new Vector(); - viewport.alignment.getSequences().setElementAt(temp, i); - viewport.alignment.getSequences().setElementAt(seq, i - 1); - } + 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) { - for (int i = viewport.alignment.getHeight() - 2; i > -1; i--) - { - SequenceI seq = viewport.alignment.getSequenceAt(i); - if (!sg.getSequences(viewport.hiddenRepSequences).contains(seq)) - { - continue; - } + 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; + } - SequenceI temp = viewport.alignment.getSequenceAt(i + 1); - if (sg.getSequences(viewport.hiddenRepSequences).contains(temp)) - { - continue; - } + if (groupAdjustment != 0) + { + viewport.getSelectionGroup().setStartRes( + viewport.getSelectionGroup().getStartRes() + groupAdjustment); + viewport.getSelectionGroup().setEndRes( + viewport.getSelectionGroup().getEndRes() + groupAdjustment); + } - viewport.alignment.getSequences().setElementAt(temp, i); - viewport.alignment.getSequences().setElementAt(seq, i + 1); - } + boolean appendHistoryItem = false; + if (viewport.historyList != null && viewport.historyList.size() > 0 + && viewport.historyList.peek() instanceof SlideSequencesCommand) + { + appendHistoryItem = ssc + .appendSlideCommand((SlideSequencesCommand) viewport.historyList + .peek()); } - alignPanel.repaint(); + if (!appendHistoryItem) + addHistoryItem(ssc); + + repaint(); } static StringBuffer copiedSequences; + static Vector copiedHiddenColumns; + protected void copy_actionPerformed() { if (viewport.getSelectionGroup() == null) @@ -1195,26 +1604,25 @@ public class AlignFrame for (int i = 0; i < sg.getSize(); i++) { SequenceI seq = sg.getSequenceAt(i); - int index = viewport.alignment.findIndex(seq); + int index = viewport.getAlignment().findIndex(seq); orderedSeqs.put(index + "", seq); } int index = 0, startRes, endRes; char ch; - if (viewport.hasHiddenColumns && viewport.getSelectionGroup() != null) + if (viewport.hasHiddenColumns() && viewport.getSelectionGroup() != null) { copiedHiddenColumns = new Vector(); int hiddenOffset = viewport.getSelectionGroup().getStartRes(); - for (int i = 0; i < viewport.getColumnSelection().getHiddenColumns().size(); - i++) + for (int i = 0; i < viewport.getColumnSelection().getHiddenColumns() + .size(); i++) { - int[] region = (int[]) - viewport.getColumnSelection().getHiddenColumns().elementAt(i); + int[] region = (int[]) viewport.getColumnSelection() + .getHiddenColumns().elementAt(i); copiedHiddenColumns.addElement(new int[] - {region[0] - hiddenOffset, - region[1] - hiddenOffset}); + { region[0] - hiddenOffset, region[1] - hiddenOffset }); } } else @@ -1241,18 +1649,18 @@ public class AlignFrame } } - //FIND START RES - //Returns residue following index if gap + // 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 + // 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))) + if (!jalview.util.Comparison.isGap((ch))) { endRes++; } @@ -1263,11 +1671,14 @@ public class AlignFrame endRes += seq.getStart() - 1; } - copiedSequences.append(seq.getName() + "\t" + - startRes + "\t" + - endRes + "\t" + - seq.getSequenceAsString(sg.getStartRes(), - sg.getEndRes() + 1) + "\n"); + copiedSequences.append(seq.getName() + + "\t" + + startRes + + "\t" + + endRes + + "\t" + + seq.getSequenceAsString(sg.getStartRes(), + sg.getEndRes() + 1) + "\n"); } } @@ -1319,9 +1730,7 @@ public class AlignFrame newtitle = newtitle.concat("- from " + getTitle()); } AlignFrame af = new AlignFrame(new Alignment(newSeqs), - viewport.applet, - newtitle, - false); + viewport.applet, newtitle, false); if (copiedHiddenColumns != null) { for (int i = 0; i < copiedHiddenColumns.size(); i++) @@ -1332,16 +1741,16 @@ public class AlignFrame } jalview.bin.JalviewLite.addFrame(af, newtitle, DEFAULT_WIDTH, - DEFAULT_HEIGHT); + DEFAULT_HEIGHT); } else { addSequences(newSeqs); } - } - catch (Exception ex) - {} // could be anything being pasted in here + } catch (Exception ex) + { + } // could be anything being pasted in here } @@ -1349,23 +1758,18 @@ public class AlignFrame { for (int i = 0; i < seqs.length; i++) { - viewport.alignment.addSequence(seqs[i]); + viewport.getAlignment().addSequence(seqs[i]); } - //!newAlignment - addHistoryItem(new EditCommand( - "Add sequences", - EditCommand.PASTE, - seqs, - 0, - viewport.alignment.getWidth(), - viewport.alignment) - ); + // !newAlignment + addHistoryItem(new EditCommand("Add sequences", EditCommand.PASTE, + seqs, 0, viewport.getAlignment().getWidth(), + viewport.getAlignment())); - viewport.setEndSeq(viewport.alignment.getHeight()); - viewport.alignment.getWidth(); - viewport.firePropertyChange("alignment", null, - viewport.alignment.getSequences()); + viewport.setEndSeq(viewport.getAlignment().getHeight()); + viewport.getAlignment().getWidth(); + viewport.firePropertyChange("alignment", null, viewport.getAlignment() + .getSequences()); } @@ -1393,10 +1797,10 @@ public class AlignFrame } // If the cut affects all sequences, remove highlighted columns - if (sg.getSize() == viewport.alignment.getHeight()) + if (sg.getSize() == viewport.getAlignment().getHeight()) { viewport.getColumnSelection().removeElements(sg.getStartRes(), - sg.getEndRes() + 1); + sg.getEndRes() + 1); } SequenceI[] cut = new SequenceI[seqs.size()]; @@ -1406,34 +1810,121 @@ public class AlignFrame } /* - //ADD HISTORY ITEM + * //ADD HISTORY ITEM */ - addHistoryItem(new EditCommand("Cut Sequences", - EditCommand.CUT, - cut, - sg.getStartRes(), - sg.getEndRes() - sg.getStartRes() + 1, - viewport.alignment)); + addHistoryItem(new EditCommand("Cut Sequences", EditCommand.CUT, cut, + sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1, + viewport.getAlignment())); viewport.setSelectionGroup(null); - viewport.alignment.deleteGroup(sg); + viewport.getAlignment().deleteGroup(sg); - viewport.firePropertyChange("alignment", null, - viewport.getAlignment().getSequences()); + 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 (viewport.getSelectionGroup() != null) + { + SequenceGroup[] gps = jalview.analysis.Grouping.makeGroupsFrom( + viewport.getSequenceSelection(), + viewport.getAlignmentView(true).getSequenceStrings( + viewport.getGapCharacter()), viewport.getAlignment() + .getGroups()); + viewport.getAlignment().deleteAllGroups(); + viewport.sequenceColours = null; + viewport.setSelectionGroup(null); + // set view properties for each group + for (int g = 0; g < gps.length; g++) + { + // gps[g].setShowunconserved(viewport.getShowUnconserved()); + gps[g].setshowSequenceLogo(viewport.isShowSequenceLogo()); + viewport.getAlignment().addGroup(gps[g]); + Color col = new Color((int) (Math.random() * 255), + (int) (Math.random() * 255), (int) (Math.random() * 255)); + col = col.brighter(); + for (SequenceI sq : gps[g].getSequences(null)) + viewport.setSequenceColour(sq, col); + } + PaintRefresher.Refresh(this, viewport.getSequenceSetId()); + alignPanel.updateAnnotation(); + alignPanel.paintAlignment(true); + } } protected void deleteGroups_actionPerformed() { - viewport.alignment.deleteAllGroups(); + viewport.getAlignment().deleteAllGroups(); viewport.sequenceColours = null; viewport.setSelectionGroup(null); - alignPanel.repaint(); + alignPanel.paintAlignment(true); } public void selectAllSequenceMenuItem_actionPerformed() @@ -1443,10 +1934,11 @@ public class AlignFrame { sg.addSequence(viewport.getAlignment().getSequenceAt(i), false); } - sg.setEndRes(viewport.alignment.getWidth() - 1); + sg.setEndRes(viewport.getAlignment().getWidth() - 1); viewport.setSelectionGroup(sg); - alignPanel.repaint(); + alignPanel.paintAlignment(true); PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId()); + viewport.sendSelection(); } public void deselectAllSequenceMenuItem_actionPerformed() @@ -1461,8 +1953,9 @@ public class AlignFrame viewport.setSelectionGroup(null); alignPanel.idPanel.idCanvas.searchResults = null; alignPanel.seqPanel.seqCanvas.highlightSearchResults(null); - alignPanel.repaint(); + alignPanel.paintAlignment(true); PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId()); + viewport.sendSelection(); } public void invertSequenceMenuItem_actionPerformed() @@ -1474,6 +1967,15 @@ public class AlignFrame } PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId()); + viewport.sendSelection(); + } + + public void invertColSel_actionPerformed() + { + viewport.invertColumnSelection(); + alignPanel.paintAlignment(true); + PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId()); + viewport.sendSelection(); } void trimAlignment(boolean trimLeft) @@ -1495,132 +1997,119 @@ public class AlignFrame SequenceI[] seqs; if (viewport.getSelectionGroup() != null) { - seqs = viewport.getSelectionGroup().getSequencesAsArray(viewport. - hiddenRepSequences); + seqs = viewport.getSelectionGroup().getSequencesAsArray( + viewport.getHiddenRepSequences()); } else { - seqs = viewport.alignment.getSequencesArray(); + seqs = viewport.getAlignment().getSequencesArray(); } TrimRegionCommand trimRegion; if (trimLeft) { trimRegion = new TrimRegionCommand("Remove Left", - TrimRegionCommand.TRIM_LEFT, - seqs, - column, - viewport.alignment, - viewport.colSel, - viewport.selectionGroup); + TrimRegionCommand.TRIM_LEFT, seqs, column, + viewport.getAlignment(), viewport.getColumnSelection(), + viewport.getSelectionGroup()); viewport.setStartRes(0); } else { trimRegion = new TrimRegionCommand("Remove Right", - TrimRegionCommand.TRIM_RIGHT, - seqs, - column, - viewport.alignment, - viewport.colSel, - viewport.selectionGroup); + TrimRegionCommand.TRIM_RIGHT, seqs, column, + viewport.getAlignment(), viewport.getColumnSelection(), + viewport.getSelectionGroup()); } statusBar.setText("Removed " + trimRegion.getSize() + " columns."); addHistoryItem(trimRegion); - Vector groups = viewport.alignment.getGroups(); - - for (int i = 0; i < groups.size(); i++) + for (SequenceGroup sg : viewport.getAlignment().getGroups()) { - SequenceGroup sg = (SequenceGroup) groups.elementAt(i); - - if ( (trimLeft && !sg.adjustForRemoveLeft(column)) - || (!trimLeft && !sg.adjustForRemoveRight(column))) + if ((trimLeft && !sg.adjustForRemoveLeft(column)) + || (!trimLeft && !sg.adjustForRemoveRight(column))) { - viewport.alignment.deleteGroup(sg); + viewport.getAlignment().deleteGroup(sg); } } - viewport.firePropertyChange("alignment", null, - viewport.getAlignment().getSequences()); + viewport.firePropertyChange("alignment", null, viewport + .getAlignment().getSequences()); } } public void removeGappedColumnMenuItem_actionPerformed() { - int start = 0, end = viewport.alignment.getWidth() - 1; + int start = 0, end = viewport.getAlignment().getWidth() - 1; SequenceI[] seqs; if (viewport.getSelectionGroup() != null) { - seqs = viewport.getSelectionGroup().getSequencesAsArray(viewport. - hiddenRepSequences); + seqs = viewport.getSelectionGroup().getSequencesAsArray( + viewport.getHiddenRepSequences()); start = viewport.getSelectionGroup().getStartRes(); end = viewport.getSelectionGroup().getEndRes(); } else { - seqs = viewport.alignment.getSequencesArray(); + seqs = viewport.getAlignment().getSequencesArray(); } - RemoveGapColCommand removeGapCols = - new RemoveGapColCommand("Remove Gapped Columns", - seqs, - start, end, - viewport.alignment); + RemoveGapColCommand removeGapCols = new RemoveGapColCommand( + "Remove Gapped Columns", seqs, start, end, + viewport.getAlignment()); addHistoryItem(removeGapCols); - statusBar.setText("Removed " + removeGapCols.getSize() + " empty columns."); + statusBar.setText("Removed " + removeGapCols.getSize() + + " empty columns."); - //This is to maintain viewport position on first residue - //of first sequence - SequenceI seq = viewport.alignment.getSequenceAt(0); + // This is to maintain viewport position on first residue + // of first sequence + SequenceI seq = viewport.getAlignment().getSequenceAt(0); int startRes = seq.findPosition(viewport.startRes); // ShiftList shifts; // viewport.getAlignment().removeGaps(shifts=new ShiftList()); // edit.alColumnChanges=shifts.getInverse(); // if (viewport.hasHiddenColumns) - // viewport.getColumnSelection().compensateForEdits(shifts); + // viewport.getColumnSelection().compensateForEdits(shifts); viewport.setStartRes(seq.findIndex(startRes) - 1); - viewport.firePropertyChange("alignment", null, - viewport.getAlignment().getSequences()); + viewport.firePropertyChange("alignment", null, viewport.getAlignment() + .getSequences()); } public void removeAllGapsMenuItem_actionPerformed() { - int start = 0, end = viewport.alignment.getWidth() - 1; + int start = 0, end = viewport.getAlignment().getWidth() - 1; SequenceI[] seqs; if (viewport.getSelectionGroup() != null) { - seqs = viewport.getSelectionGroup().getSequencesAsArray(viewport. - hiddenRepSequences); + seqs = viewport.getSelectionGroup().getSequencesAsArray( + viewport.getHiddenRepSequences()); start = viewport.getSelectionGroup().getStartRes(); end = viewport.getSelectionGroup().getEndRes(); } else { - seqs = viewport.alignment.getSequencesArray(); + seqs = viewport.getAlignment().getSequencesArray(); } - //This is to maintain viewport position on first residue - //of first sequence - SequenceI seq = viewport.alignment.getSequenceAt(0); + // This is to maintain viewport position on first residue + // of first sequence + SequenceI seq = viewport.getAlignment().getSequenceAt(0); int startRes = seq.findPosition(viewport.startRes); - addHistoryItem(new RemoveGapsCommand("Remove Gaps", - seqs, - start, end, - viewport.alignment)); + addHistoryItem(new RemoveGapsCommand("Remove Gaps", seqs, start, end, + viewport.getAlignment())); viewport.setStartRes(seq.findIndex(startRes) - 1); - viewport.firePropertyChange("alignment", null, - viewport.getAlignment().getSequences()); + viewport.firePropertyChange("alignment", null, viewport.getAlignment() + .getSequences()); } @@ -1629,49 +2118,51 @@ public class AlignFrame new Finder(alignPanel); } - public void newView() + /** + * 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) + if (viewport.hasHiddenRows()) { - newal = new Alignment(viewport.getAlignment(). - getHiddenSequences() - .getFullAlignment(). - getSequencesArray()); + newal = new Alignment(viewport.getAlignment().getHiddenSequences() + .getFullAlignment().getSequencesArray()); } else { - newal = new Alignment(viewport.alignment.getSequencesArray()); + newal = new Alignment(viewport.getAlignment().getSequencesArray()); } - if (viewport.alignment.getAlignmentAnnotation() != null) + if (viewport.getAlignment().getAlignmentAnnotation() != null) { - for (int i = 0; i < viewport.alignment.getAlignmentAnnotation().length; i++) + for (int i = 0; i < viewport.getAlignment().getAlignmentAnnotation().length; i++) { - if (!viewport.alignment.getAlignmentAnnotation()[i].autoCalculated) + if (!viewport.getAlignment().getAlignmentAnnotation()[i].autoCalculated) { - newal.addAnnotation(viewport.alignment.getAlignmentAnnotation()[i]); + newal.addAnnotation(viewport.getAlignment() + .getAlignmentAnnotation()[i]); } } } - AlignFrame newaf = new AlignFrame(newal, - viewport.applet, - "", - false); + AlignFrame newaf = new AlignFrame(newal, viewport.applet, "", false); - newaf.viewport.sequenceSetID = alignPanel.av.getSequenceSetId(); + newaf.viewport.setSequenceSetId(alignPanel.av.getSequenceSetId()); PaintRefresher.Register(alignPanel, alignPanel.av.getSequenceSetId()); PaintRefresher.Register(newaf.alignPanel, - newaf.alignPanel.av.getSequenceSetId()); + newaf.alignPanel.av.getSequenceSetId()); PaintRefresher.Register(newaf.alignPanel.idPanel.idCanvas, - newaf.alignPanel.av.getSequenceSetId()); + newaf.alignPanel.av.getSequenceSetId()); PaintRefresher.Register(newaf.alignPanel.seqPanel.seqCanvas, - newaf.alignPanel.av.getSequenceSetId()); + newaf.alignPanel.av.getSequenceSetId()); - Vector comps = (Vector) PaintRefresher.components.get(viewport. - getSequenceSetId()); + Vector comps = (Vector) PaintRefresher.components.get(viewport + .getSequenceSetId()); int viewSize = -1; for (int i = 0; i < comps.size(); i++) { @@ -1682,31 +2173,101 @@ public class AlignFrame } String title = new String(this.getTitle()); - if (title.indexOf("(View") > -1) + if (viewtitle != null) { - title = title.substring(0, title.indexOf("(View")); + title = viewtitle + " ( " + title + ")"; + } + else + { + if (title.indexOf("(View") > -1) + { + title = title.substring(0, title.indexOf("(View")); + } + title += "(View " + viewSize + ")"; } - - title += "(View " + viewSize + ")"; newaf.setTitle(title.toString()); newaf.viewport.historyList = viewport.historyList; newaf.viewport.redoList = viewport.redoList; + return newaf; + } + + /** + * + * @return list of feature groups on the view + */ + public String[] getFeatureGroups() + { + FeatureRenderer fr = null; + if (alignPanel != null + && (fr = alignPanel.getFeatureRenderer()) != null) + { + return fr.getGroups(); + } + return null; + } + + /** + * get sequence feature groups that are hidden or shown + * + * @param visible + * true is visible + * @return list + */ + public String[] getFeatureGroupsOfState(boolean visible) + { + FeatureRenderer fr = null; + if (alignPanel != null + && (fr = alignPanel.getFeatureRenderer()) != null) + { + return fr.getGroups(visible); + } + return null; + } + /** + * 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.showSequenceFeatures(true); + if (alignPanel != null + && (fr = alignPanel.getFeatureRenderer()) != null) + { + fr.setGroupState(groups, state); + alignPanel.seqPanel.seqCanvas.repaint(); + if (alignPanel.overviewPanel != null) + { + alignPanel.overviewPanel.updateOverviewImage(); + } + } } public void seqLimits_itemStateChanged() { viewport.setShowJVSuffix(seqLimits.getState()); alignPanel.fontChanged(); - alignPanel.repaint(); + alignPanel.paintAlignment(true); } protected void colourTextMenuItem_actionPerformed() { viewport.setColourText(colourTextMenuItem.getState()); - alignPanel.repaint(); + alignPanel.paintAlignment(true); + } + + protected void displayNonconservedMenuItem_actionPerformed() + { + viewport.setShowunconserved(displayNonconservedMenuItem.getState()); + alignPanel.paintAlignment(true); } protected void wrapMenuItem_actionPerformed() @@ -1716,7 +2277,7 @@ public class AlignFrame scaleAbove.setEnabled(wrapMenuItem.getState()); scaleLeft.setEnabled(wrapMenuItem.getState()); scaleRight.setEnabled(wrapMenuItem.getState()); - alignPanel.repaint(); + alignPanel.paintAlignment(true); } public void overviewMenuItem_actionPerformed() @@ -1731,15 +2292,20 @@ public class AlignFrame frame.add(overview); // +50 must allow for applet frame window jalview.bin.JalviewLite.addFrame(frame, "Overview " + this.getTitle(), - overview.getPreferredSize().width, - overview.getPreferredSize().height + 50); + overview.getPreferredSize().width, + overview.getPreferredSize().height + 50); frame.pack(); + final AlignmentPanel ap = alignPanel; frame.addWindowListener(new WindowAdapter() { + @Override public void windowClosing(WindowEvent e) { - alignPanel.setOverviewPanel(null); + if (ap != null) + { + ap.setOverviewPanel(null); + } }; }); @@ -1755,7 +2321,8 @@ public class AlignFrame { if (viewport.getAbovePIDThreshold()) { - threshold = SliderPanel.setPIDSliderSource(alignPanel, cs, "Background"); + threshold = SliderPanel.setPIDSliderSource(alignPanel, cs, + "Background"); cs.setThreshold(threshold, viewport.getIgnoreGapsConsensus()); @@ -1769,19 +2336,18 @@ public class AlignFrame if (viewport.getConservationSelected()) { - Alignment al = (Alignment) viewport.alignment; + Alignment al = (Alignment) viewport.getAlignment(); Conservation c = new Conservation("All", - ResidueProperties.propHash, 3, - al.getSequences(), 0, - al.getWidth() - 1); + ResidueProperties.propHash, 3, al.getSequences(), 0, + al.getWidth() - 1); c.calculate(); - c.verdict(false, viewport.ConsPercGaps); + c.verdict(false, viewport.getConsPercGaps()); cs.setConservation(c); - cs.setConservationInc(SliderPanel.setConservationSlider(alignPanel, cs, - "Background")); + cs.setConservationInc(SliderPanel.setConservationSlider(alignPanel, + cs, "Background")); } else @@ -1789,99 +2355,41 @@ public class AlignFrame cs.setConservation(null); } - cs.setConsensus(viewport.hconsensus); + cs.setConsensus(viewport.getSequenceConsensusHash()); } viewport.setGlobalColourScheme(cs); - if (viewport.getColourAppliesToAllGroups()) - { - Vector groups = viewport.alignment.getGroups(); - for (int i = 0; i < groups.size(); i++) - { - SequenceGroup sg = (SequenceGroup) groups.elementAt(i); - - if (cs == null) - { - sg.cs = null; - continue; - } - if (cs instanceof ClustalxColourScheme) - { - sg.cs = new ClustalxColourScheme( - sg.getSequences(viewport.hiddenRepSequences), - sg.getWidth()); - } - else - { - try - { - sg.cs = (ColourSchemeI) cs.getClass().newInstance(); - } - catch (Exception ex) - { - ex.printStackTrace(); - sg.cs = cs; - } - } - - if (viewport.getAbovePIDThreshold() - || cs instanceof PIDColourScheme - || cs instanceof Blosum62ColourScheme) - { - sg.cs.setThreshold(threshold, viewport.getIgnoreGapsConsensus()); - sg.cs.setConsensus(AAFrequency.calculate( - sg.getSequences(viewport.hiddenRepSequences), 0, sg.getWidth())); - } - else - { - sg.cs.setThreshold(0, viewport.getIgnoreGapsConsensus()); - } - - if (viewport.getConservationSelected()) - { - Conservation c = new Conservation("Group", - ResidueProperties.propHash, 3, - sg.getSequences(viewport. - hiddenRepSequences), 0, - viewport.alignment.getWidth() - 1); - c.calculate(); - c.verdict(false, viewport.ConsPercGaps); - sg.cs.setConservation(c); - } - else - { - sg.cs.setConservation(null); - sg.cs.setThreshold(0, viewport.getIgnoreGapsConsensus()); - } - - } - } - if (alignPanel.getOverviewPanel() != null) { alignPanel.getOverviewPanel().updateOverviewImage(); } - alignPanel.repaint(); + jalview.structure.StructureSelectionManager + .getStructureSelectionManager(viewport.applet) + .sequenceColoursChanged(alignPanel); + + alignPanel.paintAlignment(true); } protected void modifyPID_actionPerformed() { - if (viewport.getAbovePIDThreshold() && viewport.globalColourScheme != null) + if (viewport.getAbovePIDThreshold() + && viewport.getGlobalColourScheme() != null) { - SliderPanel.setPIDSliderSource(alignPanel, viewport.getGlobalColourScheme(), - "Background"); + SliderPanel.setPIDSliderSource(alignPanel, + viewport.getGlobalColourScheme(), "Background"); SliderPanel.showPIDSlider(); } } protected void modifyConservation_actionPerformed() { - if (viewport.getConservationSelected() && viewport.globalColourScheme != null) + if (viewport.getConservationSelected() + && viewport.getGlobalColourScheme() != null) { - SliderPanel.setConservationSlider(alignPanel, viewport.globalColourScheme, - "Background"); + SliderPanel.setConservationSlider(alignPanel, + viewport.getGlobalColourScheme(), "Background"); SliderPanel.showConservationSlider(); } } @@ -1913,27 +2421,39 @@ public class AlignFrame public void sortPairwiseMenuItem_actionPerformed() { SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray(); - AlignmentSorter.sortByPID(viewport.getAlignment(), - viewport.getAlignment().getSequenceAt(0)); + AlignmentSorter.sortByPID(viewport.getAlignment(), viewport + .getAlignment().getSequenceAt(0), null); + addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder, - viewport.alignment)); - alignPanel.repaint(); + viewport.getAlignment())); + alignPanel.paintAlignment(true); } public void sortIDMenuItem_actionPerformed() { - // addHistoryItem(new HistoryItem("ID Sort", viewport.alignment, - // HistoryItem.SORT)); + SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray(); AlignmentSorter.sortByID(viewport.getAlignment()); - alignPanel.repaint(); + addHistoryItem(new OrderCommand("ID Sort", oldOrder, + viewport.getAlignment())); + alignPanel.paintAlignment(true); + } + + public void sortLengthMenuItem_actionPerformed() + { + SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray(); + AlignmentSorter.sortByLength(viewport.getAlignment()); + addHistoryItem(new OrderCommand("Length Sort", oldOrder, + viewport.getAlignment())); + alignPanel.paintAlignment(true); } public void sortGroupMenuItem_actionPerformed() { - // addHistoryItem(new HistoryItem("Group Sort", viewport.alignment, - // HistoryItem.SORT)); + SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray(); AlignmentSorter.sortByGroup(viewport.getAlignment()); - alignPanel.repaint(); + addHistoryItem(new OrderCommand("Group Sort", oldOrder, + viewport.getAlignment())); + alignPanel.paintAlignment(true); } @@ -1945,24 +2465,24 @@ public class AlignFrame public void pairwiseAlignmentMenuItem_actionPerformed() { if (viewport.getSelectionGroup() != null - && viewport.getSelectionGroup().getSize() > 1) + && viewport.getSelectionGroup().getSize() > 1) { Frame frame = new Frame(); frame.add(new PairwiseAlignPanel(alignPanel)); - jalview.bin.JalviewLite.addFrame(frame, "Pairwise Alignment", 600, 500); + jalview.bin.JalviewLite.addFrame(frame, "Pairwise Alignment", 600, + 500); } } public void PCAMenuItem_actionPerformed() { - //are the sequences aligned? - if (!viewport.alignment.isAligned()) + // are the sequences aligned? + if (!viewport.getAlignment().isAligned(false)) { SequenceI current; int Width = viewport.getAlignment().getWidth(); - for (int i = 0; i < viewport.getAlignment().getSequences().size(); - i++) + for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++) { current = viewport.getAlignment().getSequenceAt(i); @@ -1971,13 +2491,13 @@ public class AlignFrame current.insertCharAt(Width - 1, viewport.getGapCharacter()); } } - alignPanel.repaint(); + alignPanel.paintAlignment(true); } - if ( (viewport.getSelectionGroup() != null && - viewport.getSelectionGroup().getSize() < 4 && - viewport.getSelectionGroup().getSize() > 0) - || viewport.getAlignment().getHeight() < 4) + if ((viewport.getSelectionGroup() != null + && viewport.getSelectionGroup().getSize() < 4 && viewport + .getSelectionGroup().getSize() > 0) + || viewport.getAlignment().getHeight() < 4) { return; } @@ -1985,8 +2505,7 @@ public class AlignFrame try { new PCAPanel(viewport); - } - catch (java.lang.OutOfMemoryError ex) + } catch (java.lang.OutOfMemoryError ex) { } @@ -2014,14 +2533,13 @@ public class AlignFrame void NewTreePanel(String type, String pwType, String title) { - //are the sequences aligned? - if (!viewport.alignment.isAligned()) + // are the sequences aligned? + if (!viewport.getAlignment().isAligned(false)) { SequenceI current; int Width = viewport.getAlignment().getWidth(); - for (int i = 0; i < viewport.getAlignment().getSequences().size(); - i++) + for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++) { current = viewport.getAlignment().getSequenceAt(i); @@ -2030,18 +2548,15 @@ public class AlignFrame current.insertCharAt(Width - 1, viewport.getGapCharacter()); } } - alignPanel.repaint(); + alignPanel.paintAlignment(true); } - if ( (viewport.getSelectionGroup() != null && - viewport.getSelectionGroup().getSize() > 1) - || (viewport.getSelectionGroup() == null - && viewport.alignment.getHeight() > 1)) + if ((viewport.getSelectionGroup() != null && viewport + .getSelectionGroup().getSize() > 1) + || (viewport.getAlignment().getHeight() > 1)) { - final TreePanel tp = new TreePanel(viewport, - type, - pwType); + final TreePanel tp = new TreePanel(alignPanel, type, pwType); addTreeMenuItem(tp, title); @@ -2061,31 +2576,65 @@ public class AlignFrame public void loadTree(jalview.io.NewickFile tree, String treeFile) { - TreePanel tp = new TreePanel(viewport, - treeFile, - "From File - ", - tree); + TreePanel tp = new TreePanel(alignPanel, treeFile, "From File - ", tree); jalview.bin.JalviewLite.addFrame(tp, treeFile, 600, 500); addTreeMenuItem(tp, treeFile); } - void addTreeMenuItem(final TreePanel treePanel, String title) + /** + * 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) + { + SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray(); + AlignmentSorter + .sortByTree(viewport.getAlignment(), treePanel.getTree()); + // addHistoryItem(new HistoryItem("Sort", viewport.alignment, + // HistoryItem.SORT)); + addHistoryItem(new OrderCommand("Order by " + title, oldOrder, + viewport.getAlignment())); + alignPanel.paintAlignment(true); + } + + /** + * 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) { final MenuItem item = new MenuItem(title); sortByTreeMenu.add(item); item.addActionListener(new java.awt.event.ActionListener() { + @Override public void actionPerformed(ActionEvent evt) { - // addHistoryItem(new HistoryItem("Sort", viewport.alignment, - // HistoryItem.SORT)); - AlignmentSorter.sortByTree(viewport.getAlignment(), treePanel.getTree()); - alignPanel.repaint(); + sortByTree(treePanel, title); // treePanel.getTitle()); } }); treePanel.addWindowListener(new WindowAdapter() { + @Override + public void windowOpened(WindowEvent e) + { + if (viewport.sortByTree) + { + sortByTree(treePanel, title); + } + super.windowOpened(e); + } + + @Override public void windowClosing(WindowEvent e) { sortByTreeMenu.remove(item); @@ -2093,23 +2642,45 @@ public class AlignFrame }); } + 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() + "'"); + } + AlignmentSorter.sortBy(viewport.getAlignment(), alorder); + if (undoname != null) + { + addHistoryItem(new OrderCommand(undoname, oldOrder, + viewport.getAlignment())); + } + alignPanel.paintAlignment(true); + return true; + } + protected void documentation_actionPerformed() { - showURL("http://www.jalview.org/help.html", "HELP"); + alignPanel.av.applet.openJalviewHelpUrl(); } protected void about_actionPerformed() { - class AboutPanel - extends Canvas + class AboutPanel extends Canvas { String version; - public AboutPanel(String version) + + String builddate; + + public AboutPanel(String version, String builddate) { this.version = version; + this.builddate = builddate; } + @Override public void paint(Graphics g) { g.setColor(Color.white); @@ -2119,49 +2690,39 @@ public class AlignFrame 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("Jalview - Release " + version, 200, y += fh); + g.drawString("JalviewLite - Release " + version, x, y += fh); + g.setFont(new Font("Helvetica", Font.BOLD, 12)); + g.drawString("Build date: " + builddate, x, y += fh); g.setFont(new Font("Helvetica", Font.PLAIN, 12)); - g.drawString("Authors: Michele Clamp, James Cuff, Steve Searle, Andrew Waterhouse, Jim Procter & Geoff Barton.", - x, y += fh * 2); - g.drawString("Current development managed by Andrew Waterhouse; Barton Group, University of Dundee.", - x, y += fh); g.drawString( - "For any issues relating to Jalview, email help@jalview.org", x, - y += fh); - g.drawString("If you use JalView, please cite:", x, y += fh + 8); - g.drawString("\"Clamp, M., Cuff, J., Searle, S. M. and Barton, G. J. (2004), The Jalview Java Alignment Editor\"", - x, y += fh); - g.drawString("Bioinformatics, 2004 20;426-7.", x, y += fh); - } - } - - String version = "test"; - java.net.URL url = getClass().getResource("/.build_properties"); - if (url != null) - { - try - { - BufferedReader reader = new BufferedReader(new InputStreamReader( - url.openStream())); - String line; - while ( (line = reader.readLine()) != null) - { - if (line.indexOf("VERSION") > -1) - { - version = line.substring(line.indexOf("=") + 1); - } - } - } - catch (Exception ex) - { - ex.printStackTrace(); + "Authors: Jim Procter, Andrew Waterhouse, Michele Clamp, James Cuff, Steve Searle,", + x, y += fh * 1.5); + g.drawString("David Martin & Geoff Barton.", x + 50, y += fh); + g.drawString( + "Development managed by The Barton Group, University of Dundee, Scotland, UK.", + x, y += fh); + g.drawString( + "For help, see the FAQ at www.jalview.org and/or join the jalview-discuss@jalview.org mailing list", + x, y += fh); + g.drawString("If you use Jalview, please cite:", x, y += fh + 8); + g.drawString( + "Waterhouse, A.M., Procter, J.B., Martin, D.M.A, Clamp, M. and Barton, G. J. (2009)", + x, y += fh); + g.drawString( + "Jalview Version 2 - a multiple sequence alignment editor and analysis workbench", + x, y += fh); + g.drawString("Bioinformatics doi: 10.1093/bioinformatics/btp033", + x, y += fh); } } Frame frame = new Frame(); - frame.add(new AboutPanel(version)); - jalview.bin.JalviewLite.addFrame(frame, "Jalview", 580, 200); + frame.add(new AboutPanel(JalviewLite.getVersion(), JalviewLite + .getBuildDate())); + jalview.bin.JalviewLite.addFrame(frame, "Jalview", 580, 220); } @@ -2173,118 +2734,210 @@ public class AlignFrame } 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 loadAnnotations = new MenuItem( - "Load Features/Annotations ..."); - protected MenuItem outputFeatures = new MenuItem("Export Features ..."); - protected MenuItem outputAnnotations = new MenuItem("Export Annotations ..."); - - 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(); + viewport.applet.showURL(url, target); + } + } + + // //////////////////////////////////////////////////////////////////////////////// + // JBuilder Graphics here + + MenuBar alignFrameMenuBar = new MenuBar(); + + Menu fileMenu = new Menu("File"); + + MenuItem loadApplication = new MenuItem("View in Full Application"); + + MenuItem loadTree = new MenuItem("Load Associated Tree ..."); + + MenuItem loadAnnotations = new MenuItem("Load Features/Annotations ..."); + + MenuItem outputFeatures = new MenuItem("Export Features ..."); + + MenuItem outputAnnotations = new MenuItem("Export Annotations ..."); + + MenuItem closeMenuItem = new MenuItem("Close"); + + Menu editMenu = new Menu("Edit"); + + Menu viewMenu = new Menu("View"); + + Menu colourMenu = new Menu("Colour"); + + Menu calculateMenu = new Menu("Calculate"); + + MenuItem selectAllSequenceMenuItem = new MenuItem("Select all"); + + MenuItem deselectAllSequenceMenuItem = new MenuItem("Deselect All"); + + MenuItem invertSequenceMenuItem = new MenuItem("Invert Selection"); + + MenuItem remove2LeftMenuItem = new MenuItem(); + + MenuItem remove2RightMenuItem = new MenuItem(); + + MenuItem removeGappedColumnMenuItem = new MenuItem(); + + MenuItem removeAllGapsMenuItem = new MenuItem(); + + CheckboxMenuItem viewBoxesMenuItem = new CheckboxMenuItem(); + + CheckboxMenuItem viewTextMenuItem = new CheckboxMenuItem(); + + MenuItem sortPairwiseMenuItem = new MenuItem(); + + MenuItem sortIDMenuItem = new MenuItem(); + + MenuItem sortLengthMenuItem = new MenuItem(); + + MenuItem sortGroupMenuItem = new MenuItem(); + + MenuItem removeRedundancyMenuItem = new MenuItem(); + + MenuItem pairwiseAlignmentMenuItem = new MenuItem(); + + MenuItem PCAMenuItem = new MenuItem(); + + MenuItem averageDistanceTreeMenuItem = new MenuItem(); + + MenuItem neighbourTreeMenuItem = new MenuItem(); + BorderLayout borderLayout1 = new BorderLayout(); + public Label statusBar = new Label(); - 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(); + + Menu outputTextboxMenu = new Menu(); + + MenuItem clustalColour = new MenuItem(); + + MenuItem zappoColour = new MenuItem(); + + MenuItem taylorColour = new MenuItem(); + + MenuItem hydrophobicityColour = new MenuItem(); + + MenuItem helixColour = new MenuItem(); + + MenuItem strandColour = new MenuItem(); + + MenuItem turnColour = new MenuItem(); + + MenuItem buriedColour = new MenuItem(); + + MenuItem purinePyrimidineColour = new MenuItem(); + + MenuItem RNAHelixColour = new MenuItem(); + + MenuItem userDefinedColour = new MenuItem(); + + MenuItem PIDColour = new MenuItem(); + + MenuItem BLOSUM62Colour = new MenuItem(); + + MenuItem tcoffeeColour = new MenuItem(); + MenuItem njTreeBlosumMenuItem = new MenuItem(); + MenuItem avDistanceTreeBlosumMenuItem = new MenuItem(); - protected CheckboxMenuItem annotationPanelMenuItem = new CheckboxMenuItem(); - protected CheckboxMenuItem colourTextMenuItem = new CheckboxMenuItem(); + + CheckboxMenuItem annotationPanelMenuItem = new CheckboxMenuItem(); + + CheckboxMenuItem colourTextMenuItem = new CheckboxMenuItem(); + + CheckboxMenuItem displayNonconservedMenuItem = new CheckboxMenuItem(); + + MenuItem alProperties = new MenuItem("Alignment Properties..."); + MenuItem overviewMenuItem = new MenuItem(); - protected MenuItem undoMenuItem = new MenuItem(); - protected MenuItem redoMenuItem = new MenuItem(); - protected CheckboxMenuItem conservationMenuItem = new CheckboxMenuItem(); + + MenuItem undoMenuItem = new MenuItem(); + + MenuItem redoMenuItem = new MenuItem(); + + CheckboxMenuItem conservationMenuItem = new CheckboxMenuItem(); + MenuItem noColourmenuItem = new MenuItem(); - protected CheckboxMenuItem wrapMenuItem = new CheckboxMenuItem(); - protected CheckboxMenuItem renderGapsMenuItem = new CheckboxMenuItem(); + + CheckboxMenuItem wrapMenuItem = new CheckboxMenuItem(); + + CheckboxMenuItem renderGapsMenuItem = new CheckboxMenuItem(); + MenuItem findMenuItem = new MenuItem(); - protected CheckboxMenuItem abovePIDThreshold = new CheckboxMenuItem(); - protected MenuItem nucleotideColour = new MenuItem(); + + CheckboxMenuItem abovePIDThreshold = new CheckboxMenuItem(); + + MenuItem nucleotideColour = new MenuItem(); + MenuItem deleteGroups = new MenuItem(); + + MenuItem grpsFromSelection = 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(); + + CheckboxMenuItem applyToAllGroups = new CheckboxMenuItem(); + + MenuItem font = new MenuItem(); + + CheckboxMenuItem scaleAbove = new CheckboxMenuItem(); + + CheckboxMenuItem scaleLeft = new CheckboxMenuItem(); + + CheckboxMenuItem scaleRight = new CheckboxMenuItem(); + MenuItem modifyPID = new MenuItem(); + MenuItem modifyConservation = new MenuItem(); - protected CheckboxMenuItem autoCalculate - = new CheckboxMenuItem("Autocalculate Consensus", true); - protected Menu sortByTreeMenu = new Menu(); + + CheckboxMenuItem autoCalculate = new CheckboxMenuItem( + "Autocalculate Consensus", true); + + CheckboxMenuItem sortByTree = new CheckboxMenuItem( + "Sort Alignment With New Tree", true); + + Menu sortByTreeMenu = new Menu(); + Menu sort = new Menu(); + Menu calculate = new Menu(); + MenuItem inputText = new MenuItem(); + Menu helpMenu = new Menu(); + MenuItem documentation = new MenuItem(); + MenuItem about = new MenuItem(); - protected CheckboxMenuItem seqLimits = new CheckboxMenuItem(); - Panel embeddedMenu; - Label embeddedEdit; - Label embeddedSelect; - Label embeddedView; - Label embeddedFormat; - Label embeddedColour; - Label embeddedFile; - Label embeddedHelp; - Label embeddedCalculate; - FlowLayout flowLayout1; - - private void jbInit() - throws Exception + + CheckboxMenuItem seqLimits = new CheckboxMenuItem(); + + CheckboxMenuItem centreColumnLabelFlag = new CheckboxMenuItem(); + + CheckboxMenuItem followMouseOverFlag = new CheckboxMenuItem(); + + Menu autoAnnMenu = new Menu(); + + CheckboxMenuItem showSequenceLogo = new CheckboxMenuItem(); + + CheckboxMenuItem applyAutoAnnotationSettings = new CheckboxMenuItem(); + + CheckboxMenuItem showConsensusHistogram = new CheckboxMenuItem(); + + CheckboxMenuItem showGroupConsensus = new CheckboxMenuItem(); + + CheckboxMenuItem showGroupConservation = new CheckboxMenuItem(); + + CheckboxMenuItem normSequenceLogo = new CheckboxMenuItem(); + + private void jbInit() throws Exception { setMenuBar(alignFrameMenuBar); @@ -2292,14 +2945,15 @@ public class AlignFrame MenuItem item; // dynamically fill save as menu with available formats - for (int i = 0; i < jalview.io.AppletFormatAdapter.WRITEABLE_FORMATS.length; - i++) + for (int i = 0; i < jalview.io.AppletFormatAdapter.WRITEABLE_FORMATS.length; i++) { - item = new MenuItem(jalview.io.AppletFormatAdapter.WRITEABLE_FORMATS[i]); + item = new MenuItem( + jalview.io.AppletFormatAdapter.WRITEABLE_FORMATS[i]); item.addActionListener(new java.awt.event.ActionListener() { + @Override public void actionPerformed(ActionEvent e) { outputText_actionPerformed(e); @@ -2336,6 +2990,8 @@ public class AlignFrame sortPairwiseMenuItem.addActionListener(this); sortIDMenuItem.setLabel("by ID"); sortIDMenuItem.addActionListener(this); + sortLengthMenuItem.setLabel("by Length"); + sortLengthMenuItem.addActionListener(this); sortGroupMenuItem.setLabel("by Group"); sortGroupMenuItem.addActionListener(this); removeRedundancyMenuItem.setLabel("Remove Redundancy..."); @@ -2344,8 +3000,8 @@ public class AlignFrame pairwiseAlignmentMenuItem.addActionListener(this); PCAMenuItem.setLabel("Principal Component Analysis"); PCAMenuItem.addActionListener(this); - averageDistanceTreeMenuItem.setLabel( - "Average Distance Using % Identity"); + averageDistanceTreeMenuItem + .setLabel("Average Distance Using % Identity"); averageDistanceTreeMenuItem.addActionListener(this); neighbourTreeMenuItem.setLabel("Neighbour Joining Using % Identity"); neighbourTreeMenuItem.addActionListener(this); @@ -2370,14 +3026,22 @@ public class AlignFrame turnColour.addActionListener(this); buriedColour.setLabel("Buried Index"); buriedColour.addActionListener(this); + purinePyrimidineColour.setLabel("Purine/Pyrimidine"); + purinePyrimidineColour.addActionListener(this); + RNAHelixColour.setLabel("by RNA Helices"); + RNAHelixColour.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"); + tcoffeeColour.setLabel("T-Coffee Scores"); + tcoffeeColour.setEnabled(false); // it will enabled only if a score file is + // provided + tcoffeeColour.addActionListener(this); + avDistanceTreeBlosumMenuItem + .setLabel("Average Distance Using BLOSUM62"); avDistanceTreeBlosumMenuItem.addActionListener(this); njTreeBlosumMenuItem.setLabel("Neighbour Joining Using BLOSUM62"); njTreeBlosumMenuItem.addActionListener(this); @@ -2385,6 +3049,9 @@ public class AlignFrame annotationPanelMenuItem.addItemListener(this); colourTextMenuItem.setLabel("Colour Text"); colourTextMenuItem.addItemListener(this); + displayNonconservedMenuItem.setLabel("Show nonconserved"); + displayNonconservedMenuItem.addItemListener(this); + alProperties.addActionListener(this); overviewMenuItem.setLabel("Overview Window"); overviewMenuItem.addActionListener(this); undoMenuItem.setEnabled(false); @@ -2410,6 +3077,8 @@ public class AlignFrame nucleotideColour.addActionListener(this); deleteGroups.setLabel("Undefine Groups"); deleteGroups.addActionListener(this); + grpsFromSelection.setLabel("Make Groups for selection"); + grpsFromSelection.addActionListener(this); copy.setLabel("Copy"); copy.addActionListener(this); cut.setLabel("Cut"); @@ -2446,9 +3115,13 @@ public class AlignFrame sort.setLabel("Sort"); calculate.setLabel("Calculate Tree"); autoCalculate.addItemListener(this); + sortByTree.addItemListener(this); inputText.setLabel("Input from textbox"); inputText.addActionListener(this); - + centreColumnLabelFlag.setLabel("Centre column labels"); + centreColumnLabelFlag.addItemListener(this); + followMouseOverFlag.setLabel("Automatic Scrolling"); + followMouseOverFlag.addItemListener(this); helpMenu.setLabel("Help"); documentation.setLabel("Documentation"); documentation.addActionListener(this); @@ -2473,11 +3146,33 @@ public class AlignFrame menu2.setLabel("Hide"); hideColumns.setLabel("Selected Columns"); hideSequences.setLabel("Selected Sequences"); + hideAllButSelection.setLabel("All but Selected Region (Shift+Ctrl+H)"); + hideAllSelection.setLabel("Selected Region"); + showAllHidden.setLabel("All Sequences and Columns"); + showGroupConsensus.setLabel("Group Consensus"); + showGroupConservation.setLabel("Group Conservation"); + showConsensusHistogram.setLabel("Show Consensus Histogram"); + showSequenceLogo.setLabel("Show Consensus Logo"); + normSequenceLogo.setLabel("Normalise Consensus Logo"); + applyAutoAnnotationSettings.setLabel("Apply to all groups"); + applyAutoAnnotationSettings.setState(true); + autoAnnMenu.setLabel("Autocalculated Annotation"); + invertColSel.addActionListener(this); showColumns.addActionListener(this); showSeqs.addActionListener(this); hideColumns.addActionListener(this); hideSequences.addActionListener(this); + hideAllButSelection.addActionListener(this); + hideAllSelection.addActionListener(this); + showAllHidden.addActionListener(this); + showGroupConsensus.addItemListener(this); + showGroupConservation.addItemListener(this); + showConsensusHistogram.addItemListener(this); + showSequenceLogo.addItemListener(this); + normSequenceLogo.addItemListener(this); + + applyAutoAnnotationSettings.addItemListener(this); formatMenu.setLabel("Format"); selectMenu.setLabel("Select"); newView.setLabel("New View"); @@ -2525,11 +3220,22 @@ public class AlignFrame viewMenu.add(menu1); viewMenu.add(menu2); viewMenu.addSeparator(); + viewMenu.add(followMouseOverFlag); viewMenu.add(annotationPanelMenuItem); + autoAnnMenu.add(applyAutoAnnotationSettings); + autoAnnMenu.add(showConsensusHistogram); + autoAnnMenu.add(showSequenceLogo); + autoAnnMenu.add(normSequenceLogo); + autoAnnMenu.addSeparator(); + autoAnnMenu.add(showGroupConservation); + autoAnnMenu.add(showGroupConsensus); + viewMenu.add(autoAnnMenu); viewMenu.addSeparator(); viewMenu.add(sequenceFeatures); viewMenu.add(featureSettings); viewMenu.addSeparator(); + viewMenu.add(alProperties); + viewMenu.addSeparator(); viewMenu.add(overviewMenuItem); colourMenu.add(applyToAllGroups); colourMenu.addSeparator(); @@ -2545,6 +3251,8 @@ public class AlignFrame colourMenu.add(turnColour); colourMenu.add(buriedColour); colourMenu.add(nucleotideColour); + colourMenu.add(purinePyrimidineColour); + colourMenu.add(tcoffeeColour); colourMenu.add(userDefinedColour); colourMenu.addSeparator(); colourMenu.add(conservationMenuItem); @@ -2552,16 +3260,19 @@ public class AlignFrame colourMenu.add(abovePIDThreshold); colourMenu.add(modifyPID); colourMenu.add(annotationColour); + colourMenu.add(RNAHelixColour); calculateMenu.add(sort); calculateMenu.add(calculate); calculateMenu.addSeparator(); calculateMenu.add(pairwiseAlignmentMenuItem); calculateMenu.add(PCAMenuItem); calculateMenu.add(autoCalculate); + calculateMenu.add(sortByTree); this.add(statusBar, BorderLayout.SOUTH); pasteMenu.add(pasteNew); pasteMenu.add(pasteThis); sort.add(sortIDMenuItem); + sort.add(sortLengthMenuItem); sort.add(sortByTreeMenu); sort.add(sortGroupMenuItem); sort.add(sortPairwiseMenuItem); @@ -2573,8 +3284,11 @@ public class AlignFrame helpMenu.add(about); menu1.add(showColumns); menu1.add(showSeqs); + menu1.add(showAllHidden); menu2.add(hideColumns); menu2.add(hideSequences); + menu2.add(hideAllSelection); + menu2.add(hideAllButSelection); formatMenu.add(font); formatMenu.add(seqLimits); formatMenu.add(wrapMenuItem); @@ -2584,162 +3298,459 @@ public class AlignFrame formatMenu.add(viewBoxesMenuItem); formatMenu.add(viewTextMenuItem); formatMenu.add(colourTextMenuItem); + formatMenu.add(displayNonconservedMenuItem); formatMenu.add(renderGapsMenuItem); + formatMenu.add(centreColumnLabelFlag); selectMenu.add(findMenuItem); selectMenu.addSeparator(); selectMenu.add(selectAllSequenceMenuItem); selectMenu.add(deselectAllSequenceMenuItem); selectMenu.add(invertSequenceMenuItem); selectMenu.add(invertColSel); + selectMenu.add(grpsFromSelection); selectMenu.add(deleteGroups); + } - public void setEmbedded() - { - - embeddedMenu = new Panel(); - embeddedEdit = new Label("Edit"); - embeddedSelect = new Label("Select"); - embeddedView = new Label("View"); - embeddedFormat = new Label("Format"); - embeddedColour = new Label("Colour"); - embeddedFile = new Label("File"); - embeddedHelp = new Label("Help"); - embeddedCalculate = new Label("Calculate"); - flowLayout1 = new FlowLayout(); - embeddedMenu.setBackground(Color.lightGray); - embeddedMenu.setLayout(flowLayout1); - embeddedEdit.setFont(new java.awt.Font("Arial", Font.PLAIN, 10)); - embeddedSelect.setFont(new java.awt.Font("Arial", Font.PLAIN, 10)); - embeddedView.setFont(new java.awt.Font("Arial", Font.PLAIN, 10)); - embeddedFormat.setFont(new java.awt.Font("Arial", Font.PLAIN, 10)); - embeddedColour.setFont(new java.awt.Font("Arial", Font.PLAIN, 10)); - embeddedFile.setFont(new java.awt.Font("Arial", Font.PLAIN, 10)); - embeddedHelp.setFont(new java.awt.Font("Arial", Font.PLAIN, 10)); - embeddedCalculate.setFont(new java.awt.Font("Arial", Font.PLAIN, 10)); - embeddedMenu.add(embeddedFile); - embeddedMenu.add(embeddedEdit); - embeddedMenu.add(embeddedSelect); - embeddedMenu.add(embeddedView); - embeddedMenu.add(embeddedFormat); - embeddedMenu.add(embeddedColour); - embeddedMenu.add(embeddedCalculate); - embeddedMenu.add(embeddedHelp); - flowLayout1.setAlignment(FlowLayout.LEFT); - flowLayout1.setHgap(2); - flowLayout1.setVgap(0); - embeddedFile.addMouseListener(this); - embeddedEdit.addMouseListener(this); - embeddedSelect.addMouseListener(this); - embeddedView.addMouseListener(this); - embeddedFormat.addMouseListener(this); - embeddedColour.addMouseListener(this); - embeddedCalculate.addMouseListener(this); - embeddedHelp.addMouseListener(this); - - fileMenu.remove(closeMenuItem); - fileMenu.remove(3); // Seperator - - viewport.applet.setLayout(new BorderLayout()); - viewport.applet.add(embeddedMenu, BorderLayout.NORTH); - viewport.applet.add(statusBar, BorderLayout.SOUTH); - - alignPanel.setSize(viewport.applet.getSize().width, - viewport.applet.getSize().height - - embeddedMenu.HEIGHT - statusBar.HEIGHT); - - viewport.applet.add(alignPanel, BorderLayout.CENTER); - viewport.applet.validate(); - - } - - PopupMenu filePopup, editPopup, searchPopup, - viewPopup, formatPopup, colourPopup, calculatePopup, helpPopup; MenuItem featureSettings = new MenuItem(); + CheckboxMenuItem sequenceFeatures = new CheckboxMenuItem(); + MenuItem annotationColour = new MenuItem(); + MenuItem invertColSel = new MenuItem(); + Menu menu1 = new Menu(); + MenuItem showColumns = new MenuItem(); + MenuItem showSeqs = new MenuItem(); + Menu menu2 = new Menu(); + MenuItem hideColumns = new MenuItem(); + MenuItem hideSequences = new MenuItem(); + + MenuItem hideAllButSelection = new MenuItem(); + + MenuItem hideAllSelection = new MenuItem(); + + MenuItem showAllHidden = new MenuItem(); + Menu formatMenu = new Menu(); + Menu selectMenu = new Menu(); + MenuItem newView = new MenuItem(); - public void mousePressed(MouseEvent evt) - { - PopupMenu popup = null; - Label source = (Label) evt.getSource(); - if (source == embeddedFile) - { - popup = filePopup = genPopupMenu(filePopup, fileMenu); + /** + * Attach the alignFrame panels after embedding menus, if necessary. This used + * to be called setEmbedded, but is now creates the dropdown menus in a + * platform independent manner to avoid OSX/Mac menu appendage daftness. + * + * @param reallyEmbedded + * true to attach the view to the applet area on the page rather than + * in a new window + */ + public void createAlignFrameWindow(boolean reallyEmbedded, String title) + { + if (reallyEmbedded) + { + // //// + // Explicly 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 Seperator + embeddedMenu = makeEmbeddedPopupMenu(alignFrameMenuBar, "Arial", + Font.PLAIN, 10, false); // use our own fonts. + // and actually add the components to the applet area + viewport.applet.setLayout(new BorderLayout()); + viewport.applet.add(embeddedMenu, BorderLayout.NORTH); + viewport.applet.add(statusBar, BorderLayout.SOUTH); + alignPanel.setSize(viewport.applet.getSize().width, + viewport.applet.getSize().height - embeddedMenu.HEIGHT + - statusBar.HEIGHT); + viewport.applet.add(alignPanel, BorderLayout.CENTER); + final AlignFrame me = this; + viewport.applet.addFocusListener(new FocusListener() + { + + @Override + public void focusLost(FocusEvent e) + { + if (me.viewport.applet.currentAlignFrame == me) + { + me.viewport.applet.currentAlignFrame = null; + } + } + + @Override + public void focusGained(FocusEvent e) + { + me.viewport.applet.currentAlignFrame = me; + } + }); + viewport.applet.validate(); } - else if (source == embeddedEdit) + else { - popup = editPopup = genPopupMenu(editPopup, editMenu); + // ////// + // test and embed menu bar if necessary. + // + if (embedMenuIfNeeded(alignPanel)) + { + // adjust for status bar height too + alignPanel.setSize(getSize().width, getSize().height + - statusBar.HEIGHT); + } + 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, title, DEFAULT_WIDTH, + DEFAULT_HEIGHT); } - else if (source == embeddedSelect) + } + + /** + * 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) + { + org.jmol.api.JmolViewer viewer = null; + try + { + viewer = (org.jmol.api.JmolViewer) jmolviewer; + } catch (ClassCastException ex) { - popup = searchPopup = genPopupMenu(searchPopup, selectMenu); + System.err.println("Unsupported viewer object :" + + jmolviewer.getClass()); } - else if (source == embeddedView) + if (viewer == null) { - popup = viewPopup = genPopupMenu(viewPopup, viewMenu); + System.err.println("Can't use this object as a structure viewer:" + + jmolviewer.getClass()); + return null; } - else if (source == embeddedFormat) + SequenceI[] seqs = null; + if (sequenceIds == null || sequenceIds.length == 0) { - popup = formatPopup = genPopupMenu(formatPopup, formatMenu); + seqs = viewport.getAlignment().getSequencesArray(); } - else if (source == embeddedColour) + else { - popup = colourPopup = genPopupMenu(colourPopup, colourMenu); + Vector sqi = new Vector(); + AlignmentI al = viewport.getAlignment(); + for (int sid = 0; sid < sequenceIds.length; sid++) + { + SequenceI sq = al.findName(sequenceIds[sid]); + if (sq != null) + { + sqi.addElement(sq); + } + } + 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; + } } - else if (source == embeddedCalculate) + ExtJmol 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; + + } + + /** + * 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) + { + SequenceI toaddpdb = viewport.getAlignment().findName(sequenceId); + boolean needtoadd = false; + if (toaddpdb != null) { - popup = calculatePopup = genPopupMenu(calculatePopup, calculateMenu); + Vector pdbe = toaddpdb.getPDBId(); + 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 + String protocol = AppletFormatAdapter.resolveProtocol(pdbFile, "PDB"); + if (protocol == null) + { + return false; + } + if (needtoadd) + { + // make a note of the access mode and add + if (pdbentry.getProperty() == null) + { + pdbentry.setProperty(new Hashtable()); + } + pdbentry.getProperty().put("protocol", protocol); + toaddpdb.addPDBId(pdbentry); + } } - else if (source == embeddedHelp) + return true; + } + + private Object[] cleanSeqChainArrays(SequenceI[] seqs, String[] chains) + { + if (seqs != null) { - popup = helpPopup = genPopupMenu(helpPopup, helpMenu); + Vector sequences = new Vector(); + for (int i = 0; i < seqs.length; i++) + { + if (seqs[i] != null) + { + sequences.addElement(new Object[] + { seqs[i], (chains != null) ? chains[i] : null }); + } + } + seqs = new SequenceI[sequences.size()]; + chains = new String[sequences.size()]; + for (int i = 0, isize = sequences.size(); i < isize; i++) + { + Object[] oj = (Object[]) sequences.elementAt(i); + + seqs[i] = (SequenceI) oj[0]; + chains[i] = (String) oj[1]; + } } + return new Object[] + { seqs, chains }; - embeddedMenu.add(popup); - popup.show(embeddedMenu, - source.getBounds().x, - source.getBounds().y + source.getBounds().getSize().height); } - PopupMenu genPopupMenu(PopupMenu popup, Menu original) + public void newStructureView(JalviewLite applet, PDBEntry pdb, + SequenceI[] seqs, String[] chains, String protocol) { - if (popup != null) + // 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) + { + System.err + .println("JalviewLite.AlignFrame:newStructureView: No sequence to bind structure to."); + } + if (protocol == null || protocol.trim().length() == 0 + || protocol.equals("null")) + { + protocol = (String) pdb.getProperty().get("protocol"); + if (protocol == null) + { + System.err.println("Couldn't work out protocol to open structure: " + + pdb.getId()); + return; + } + } + if (applet.useXtrnalSviewer) + { + // 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 + jalview.appletgui.AppletJmol ajm = null, tajm; + Vector jmols = applet + .getAppletWindow(jalview.appletgui.AppletJmol.class); + for (int i = 0, iSize = jmols.size(); i < iSize; i++) + { + tajm = (jalview.appletgui.AppletJmol) jmols.elementAt(i); + if (tajm.ap.alignFrame == this) + { + ajm = tajm; + break; + } + } + if (ajm != null) + { + 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; + } + } + // otherwise, create a new window + if (applet.jmolAvailable) { - return popup; + new jalview.appletgui.AppletJmol(pdb, seqs, chains, alignPanel, + protocol); + applet.lastFrameX += 40; + applet.lastFrameY += 40; } - popup = new PopupMenu(); - int m, mSize = original.getItemCount(); - for (m = 0; m < mSize; m++) + else { - popup.add(original.getItem(m)); - mSize--; - m--; + new MCview.AppletPDBViewer(pdb, seqs, chains, alignPanel, protocol); } - return popup; } - public void mouseClicked(MouseEvent evt) - {} + 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."); + } + + /** + * 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); + } + + /** + * @return the alignments unique ID. + */ + public String getSequenceSetId() + { + return viewport.getSequenceSetId(); + } + + /** + * 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 + { + + TCoffeeScoreFile file = new TCoffeeScoreFile(source, + AppletFormatAdapter.checkProtocol(source)); + if (!file.isValid()) + { + // TODO: raise dialog for gui + System.err.println("Problems parsing T-Coffee scores: " + + file.getWarningMessage()); + System.err.println("Origin was:\n" + source); + return false; + } - public void mouseReleased(MouseEvent evt) - {} + /* + * check that the score matrix matches the alignment dimensions + */ + AlignmentI aln; + if ((aln = viewport.getAlignment()) != null + && (aln.getHeight() != file.getHeight() || aln.getWidth() != file + .getWidth())) + { + // TODO: raise a dialog box here rather than bomb out. + System.err + .println("The scores matrix does not match the alignment dimensions"); - public void mouseEntered(MouseEvent evt) - {} + } - public void mouseExited(MouseEvent evt) - {} + // TODO add parameter to indicate if matching should be done + if (file.annotateAlignment(alignPanel.getAlignment(), false)) + { + alignPanel.fontChanged(); + tcoffeeColour.setEnabled(true); + // switch to this color + changeColour(new TCoffeeColourScheme(alignPanel.getAlignment())); + return true; + } + else + { + System.err.println("Problems resolving T-Coffee scores:"); + if (file.getWarningMessage() != null) + { + System.err.println(file.getWarningMessage()); + } + } + return false; + } }