X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FAlignFrame.java;h=0aefe9b01b51d544ce42103ceb58fea4f0c904a2;hb=90a1b20c1297ec0d7fc596f89f6323a4b1bc7083;hp=1b2088e765cdcb428ee263fa0067ce9af4eec2bf;hpb=2ac096ecd8ee1a5c11480e864fce7cf78d661c66;p=jalview.git diff --git a/src/jalview/appletgui/AlignFrame.java b/src/jalview/appletgui/AlignFrame.java index 1b2088e..0aefe9b 100755 --- a/src/jalview/appletgui/AlignFrame.java +++ b/src/jalview/appletgui/AlignFrame.java @@ -1,20 +1,19 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) - * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5) + * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle * - * This program is free software; you can redistribute it and/or - * modify it under the terms of the GNU General Public License - * as published by the Free Software Foundation; either version 2 - * of the License, or (at your option) any later version. + * This file is part of Jalview. * - * 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 free software: you can redistribute it and/or + * modify it under the terms of the GNU General Public License + * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. * - * 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 + * Jalview is distributed in the hope that it will be useful, but + * WITHOUT ANY WARRANTY; without even the implied warranty + * of MERCHANTABILITY or FITNESS FOR A PARTICULAR + * PURPOSE. See the GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License along with Jalview. If not, see . */ package jalview.appletgui; @@ -86,6 +85,10 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, { sortPairwiseMenuItem_actionPerformed(); } + else if (param.equalsIgnoreCase("Length")) + { + sortLengthMenuItem_actionPerformed(); + } } param = applet.getParameter("wrap"); @@ -150,7 +153,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, * DOCUMENT ME! * * @param String - * DOCUMENT ME! + * DOCUMENT ME! */ public void parseFeaturesFile(String file, String type) @@ -176,7 +179,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, } viewport.showSequenceFeatures = true; sequenceFeatures.setState(true); - if (viewport.featureSettings!=null) + if (viewport.featureSettings != null) { viewport.featureSettings.refreshTable(); } @@ -441,13 +444,14 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, } alignPanel.paintAlignment(true); } + /** * called by key handler and the hide all/show all menu items + * * @param toggleSeqs * @param toggleCols */ - private void toggleHiddenRegions(boolean toggleSeqs, - boolean toggleCols) + private void toggleHiddenRegions(boolean toggleSeqs, boolean toggleCols) { boolean hide = false; SequenceGroup sg = viewport.getSelectionGroup(); @@ -456,8 +460,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, // 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.colSel != null - && viewport.colSel.getSelected() != null && viewport.colSel + if ((viewport.colSel != null && viewport.colSel.getSelected() != null && viewport.colSel .getSelected().size() > 0) || (sg != null && sg.getSize() > 0 && sg.getStartRes() <= sg .getEndRes())) @@ -508,6 +511,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, } } } + public void keyReleased(KeyEvent evt) { } @@ -587,7 +591,8 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, else if (evt.getSource() == this.centreColumnLabelFlag) { centreColumnLabelFlag_stateChanged(); - } else if (evt.getSource() == this.followMouseOverFlag) + } + else if (evt.getSource() == this.followMouseOverFlag) { mouseOverFlag_stateChanged(); } @@ -598,7 +603,8 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, private void mouseOverFlag_stateChanged() { viewport.followHighlight = followMouseOverFlag.getState(); - // TODO: could kick the scrollTo mechanism to reset view for current searchresults. + // TODO: could kick the scrollTo mechanism to reset view for current + // searchresults. } private void centreColumnLabelFlag_stateChanged() @@ -761,18 +767,21 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, viewport.hideAllSelectedSeqs(); alignPanel.paintAlignment(true); } - else if (source == hideAllButSelection) { - toggleHiddenRegions(false,false); + else if (source == hideAllButSelection) + { + toggleHiddenRegions(false, false); alignPanel.paintAlignment(true); } - else if (source == hideAllSelection) { + else if (source == hideAllSelection) + { SequenceGroup sg = viewport.getSelectionGroup(); viewport.expandColSelection(sg, false); viewport.hideAllSelectedSeqs(); viewport.hideSelectedColumns(); alignPanel.paintAlignment(true); } - else if (source == showAllHidden) { + else if (source == showAllHidden) + { viewport.showAllHiddenColumns(); viewport.showAllHiddenSeqs(); alignPanel.paintAlignment(true); @@ -900,6 +909,10 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, { sortIDMenuItem_actionPerformed(); } + else if (source == sortLengthMenuItem) + { + sortLengthMenuItem_actionPerformed(); + } else if (source == sortGroupMenuItem) { sortGroupMenuItem_actionPerformed(); @@ -996,14 +1009,15 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, private Hashtable getDisplayedFeatureCols() { - if (alignPanel.getFeatureRenderer()!=null) { + if (alignPanel.getFeatureRenderer() != 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)); + fcols.put(col, fr.featureColours.get(col)); } return fcols; } @@ -1191,7 +1205,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, * DOCUMENT ME! * * @param e - * DOCUMENT ME! + * DOCUMENT ME! */ protected void undoMenuItem_actionPerformed() { @@ -1216,7 +1230,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, * DOCUMENT ME! * * @param e - * DOCUMENT ME! + * DOCUMENT ME! */ protected void redoMenuItem_actionPerformed() { @@ -1653,6 +1667,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, this.setVisible(false); } } + protected void makeGrpsFromSelection_actionPerformed() { if (viewport.getSelectionGroup() != null) @@ -1668,7 +1683,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, for (int g = 0; g < gps.length; g++) { // gps[g].setShowunconserved(viewport.getShowUnconserved()); - gps[g].setIncludeAllConsSymbols(viewport.isIncludeAllConsensusSymbols()); + gps[g].setshowSequenceLogo(viewport.isShowSequenceLogo()); viewport.alignment.addGroup(gps[g]); Color col = new Color((int) (Math.random() * 255), (int) (Math .random() * 255), (int) (Math.random() * 255)); @@ -1683,6 +1698,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, alignPanel.paintAlignment(true); } } + protected void deleteGroups_actionPerformed() { viewport.alignment.deleteAllGroups(); @@ -1731,6 +1747,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId()); } + public void invertColSel_actionPerformed() { viewport.invertColumnSelection(); @@ -1976,7 +1993,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, * get sequence feature groups that are hidden or shown * * @param visible - * true is visible + * true is visible * @return list */ public String[] getFeatureGroupsOfState(boolean visible) @@ -1994,9 +2011,9 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, * Change the display state for the given feature groups * * @param groups - * list of group strings + * list of group strings * @param state - * visible or invisible + * visible or invisible */ public void setFeatureGroupState(String[] groups, boolean state) { @@ -2238,6 +2255,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, modifyPID_actionPerformed(); } + public void sortPairwiseMenuItem_actionPerformed() { SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray(); @@ -2253,8 +2271,15 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, { SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray(); AlignmentSorter.sortByID(viewport.getAlignment()); - addHistoryItem(new OrderCommand("ID Sort", oldOrder, - viewport.alignment)); + addHistoryItem(new OrderCommand("ID Sort", oldOrder, viewport.alignment)); + alignPanel.paintAlignment(true); + } + + public void sortLengthMenuItem_actionPerformed() + { + SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray(); + AlignmentSorter.sortByLength(viewport.getAlignment()); + addHistoryItem(new OrderCommand("Length Sort", oldOrder, viewport.alignment)); alignPanel.paintAlignment(true); } @@ -2392,28 +2417,36 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, jalview.bin.JalviewLite.addFrame(tp, treeFile, 600, 500); addTreeMenuItem(tp, treeFile); } + /** * sort the alignment using the given treePanel - * @param treePanel tree used to sort view - * @param title string used for undo event name + * + * @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()); + AlignmentSorter + .sortByTree(viewport.getAlignment(), treePanel.getTree()); // addHistoryItem(new HistoryItem("Sort", viewport.alignment, // HistoryItem.SORT)); - addHistoryItem(new OrderCommand("Order by "+title, oldOrder, + addHistoryItem(new OrderCommand("Order by " + title, oldOrder, viewport.alignment)); alignPanel.paintAlignment(true); } + /** - * Do any automatic reordering of the alignment and add the necessary bits to the menu structure for the new tree + * 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) + protected void addTreeMenuItem(final TreePanel treePanel, + final String title) { final MenuItem item = new MenuItem(title); sortByTreeMenu.add(item); @@ -2454,7 +2487,9 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, class AboutPanel extends Canvas { String version; + String builddate; + public AboutPanel(String version, String builddate) { this.version = version; @@ -2475,7 +2510,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, g.setFont(new Font("Helvetica", Font.BOLD, 14)); 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.drawString("Build date: " + builddate, x, y += fh); g.setFont(new Font("Helvetica", Font.PLAIN, 12)); g .drawString( @@ -2491,15 +2526,22 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, "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); + 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(JalviewLite.getVersion(), JalviewLite.getBuildDate())); + frame.add(new AboutPanel(JalviewLite.getVersion(), JalviewLite + .getBuildDate())); jalview.bin.JalviewLite.addFrame(frame, "Jalview", 580, 220); } @@ -2514,18 +2556,25 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, { try { - if (url.indexOf(":")==-1) + if (url.indexOf(":") == -1) { - // TODO: verify (Bas Vroling bug) prepend codebase or server URL to form valid URL - if (url.indexOf("/")==0) + // TODO: verify (Bas Vroling bug) prepend codebase or server URL to + // form valid URL + if (url.indexOf("/") == 0) { String codebase = viewport.applet.getCodeBase().toString(); - url = codebase.substring(0,codebase.length()-viewport.applet.getCodeBase().getFile().length())+url; - } else { - url = viewport.applet.getCodeBase()+url; + url = codebase.substring(0, codebase.length() + - viewport.applet.getCodeBase().getFile().length()) + + url; + } + else + { + url = viewport.applet.getCodeBase() + url; } System.out.println("Show url (prepended codebase): " + url); - } else { + } + else + { System.out.println("Show url: " + url); } viewport.applet.getAppletContext().showDocument( @@ -2586,6 +2635,8 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, MenuItem sortIDMenuItem = new MenuItem(); + MenuItem sortLengthMenuItem = new MenuItem(); + MenuItem sortGroupMenuItem = new MenuItem(); MenuItem removeRedundancyMenuItem = new MenuItem(); @@ -2660,7 +2711,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, MenuItem deleteGroups = new MenuItem(); - MenuItem grpsFromSelection= new MenuItem(); + MenuItem grpsFromSelection = new MenuItem(); MenuItem delete = new MenuItem(); @@ -2763,6 +2814,8 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, 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..."); @@ -2812,7 +2865,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, annotationPanelMenuItem.addItemListener(this); colourTextMenuItem.setLabel("Colour Text"); colourTextMenuItem.addItemListener(this); - displayNonconservedMenuItem.setLabel("Show non-conserved"); + displayNonconservedMenuItem.setLabel("Show nonconserved"); displayNonconservedMenuItem.addItemListener(this); alProperties.addActionListener(this); overviewMenuItem.setLabel("Overview Window"); @@ -3006,6 +3059,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, pasteMenu.add(pasteNew); pasteMenu.add(pasteThis); sort.add(sortIDMenuItem); + sort.add(sortLengthMenuItem); sort.add(sortByTreeMenu); sort.add(sortGroupMenuItem); sort.add(sortPairwiseMenuItem); @@ -3042,7 +3096,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, selectMenu.add(invertColSel); selectMenu.add(grpsFromSelection); selectMenu.add(deleteGroups); - + } MenuItem featureSettings = new MenuItem(); @@ -3066,7 +3120,9 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, MenuItem hideSequences = new MenuItem(); MenuItem hideAllButSelection = new MenuItem(); + MenuItem hideAllSelection = new MenuItem(); + MenuItem showAllHidden = new MenuItem(); Menu formatMenu = new Menu(); @@ -3081,8 +3137,8 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, * 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 + * 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) {