X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fjbgui%2FGAlignFrame.java;h=83426091b64ff64398712d9537a8969b95f3353d;hb=a8a602a77b811d88cdbbfdb90d8fa6984b9344ae;hp=2325de1dd37e5eee4fe55d4d5659bd191509a0b6;hpb=aff93619ba53584f9b01970832558331951d9dbf;p=jalview.git diff --git a/src/jalview/jbgui/GAlignFrame.java b/src/jalview/jbgui/GAlignFrame.java index 2325de1..8342609 100755 --- a/src/jalview/jbgui/GAlignFrame.java +++ b/src/jalview/jbgui/GAlignFrame.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.jbgui; @@ -122,7 +121,7 @@ public class GAlignFrame extends JInternalFrame public JCheckBoxMenuItem colourTextMenuItem = new JCheckBoxMenuItem(); - public JCheckBoxMenuItem showUnconservedMenuItem = new JCheckBoxMenuItem(); + public JCheckBoxMenuItem showNonconservedMenuItem = new JCheckBoxMenuItem(); JMenuItem htmlMenuItem = new JMenuItem(); @@ -147,6 +146,7 @@ public class GAlignFrame extends JInternalFrame public JCheckBoxMenuItem abovePIDThreshold = new JCheckBoxMenuItem(); public JCheckBoxMenuItem showSeqFeatures = new JCheckBoxMenuItem(); + public JCheckBoxMenuItem showSeqFeaturesHeight = new JCheckBoxMenuItem(); protected JRadioButtonMenuItem nucleotideColour = new JRadioButtonMenuItem(); @@ -196,7 +196,9 @@ public class GAlignFrame extends JInternalFrame JMenu jMenu2 = new JMenu(); protected JCheckBoxMenuItem padGapsMenuitem = new JCheckBoxMenuItem(); + protected JCheckBoxMenuItem showNpFeatsMenuitem = new JCheckBoxMenuItem(); + protected JCheckBoxMenuItem showDbRefsMenuitem = new JCheckBoxMenuItem(); protected ButtonGroup colours = new ButtonGroup(); @@ -236,7 +238,7 @@ public class GAlignFrame extends JInternalFrame GridLayout gridLayout1 = new GridLayout(); JMenu jMenu3 = new JMenu(); - + JMenuItem showAllSeqs = new JMenuItem(); JMenuItem showAllColumns = new JMenuItem(); @@ -276,7 +278,7 @@ public class GAlignFrame extends JInternalFrame protected JCheckBoxMenuItem centreColumnLabelsMenuItem = new JCheckBoxMenuItem(); protected JCheckBoxMenuItem followHighlightMenuItem = new JCheckBoxMenuItem(); - + protected JMenuItem gatherViews = new JMenuItem(); protected JMenuItem expandViews = new JMenuItem(); @@ -284,21 +286,27 @@ public class GAlignFrame extends JInternalFrame JMenuItem pageSetup = new JMenuItem(); JMenuItem alignmentProperties = new JMenuItem(); - + JMenu tooltipSettingsMenu = new JMenu(); - private JMenuItem justifyLeftMenuItem=new JMenuItem(); + private JMenuItem justifyLeftMenuItem = new JMenuItem(); - private JMenuItem justifyRightMenuItem=new JMenuItem(); + private JMenuItem justifyRightMenuItem = new JMenuItem(); JMenu autoAnnMenu = new JMenu(); - protected JCheckBoxMenuItem showGroupConsensus=new JCheckBoxMenuItem(); - protected JCheckBoxMenuItem showGroupConservation=new JCheckBoxMenuItem(); - protected JCheckBoxMenuItem showConsensusHistogram=new JCheckBoxMenuItem(); - protected JCheckBoxMenuItem showSequenceLogo=new JCheckBoxMenuItem(); - protected JCheckBoxMenuItem applyAutoAnnotationSettings=new JCheckBoxMenuItem(); + + protected JCheckBoxMenuItem showGroupConsensus = new JCheckBoxMenuItem(); + + protected JCheckBoxMenuItem showGroupConservation = new JCheckBoxMenuItem(); + + protected JCheckBoxMenuItem showConsensusHistogram = new JCheckBoxMenuItem(); + + protected JCheckBoxMenuItem showSequenceLogo = new JCheckBoxMenuItem(); + + protected JCheckBoxMenuItem applyAutoAnnotationSettings = new JCheckBoxMenuItem(); private JMenuItem grpsFromSelection = new JMenuItem(); + public GAlignFrame() { try @@ -560,7 +568,7 @@ public class GAlignFrame extends JInternalFrame public void actionPerformed(ActionEvent e) { makeGrpsFromSelection_actionPerformed(e); - } + } }); remove2LeftMenuItem.setText("Remove Left"); @@ -613,21 +621,23 @@ public class GAlignFrame extends JInternalFrame } }); justifyLeftMenuItem.setText("Left Justify Alignment"); - justifyLeftMenuItem.addActionListener(new java.awt.event.ActionListener() - { - public void actionPerformed(ActionEvent e) - { - justifyLeftMenuItem_actionPerformed(e); - } - }); + justifyLeftMenuItem + .addActionListener(new java.awt.event.ActionListener() + { + public void actionPerformed(ActionEvent e) + { + justifyLeftMenuItem_actionPerformed(e); + } + }); justifyRightMenuItem.setText("Right Justify Alignment"); - justifyRightMenuItem.addActionListener(new java.awt.event.ActionListener() - { - public void actionPerformed(ActionEvent e) - { - justifyRightMenuItem_actionPerformed(e); - } - }); + justifyRightMenuItem + .addActionListener(new java.awt.event.ActionListener() + { + public void actionPerformed(ActionEvent e) + { + justifyRightMenuItem_actionPerformed(e); + } + }); viewBoxesMenuItem.setText("Boxes"); viewBoxesMenuItem.setState(true); viewBoxesMenuItem.addActionListener(new java.awt.event.ActionListener() @@ -646,15 +656,16 @@ public class GAlignFrame extends JInternalFrame viewTextMenuItem_actionPerformed(e); } }); - showUnconservedMenuItem.setText("Show Unconserved"); - showUnconservedMenuItem.setState(false); - showUnconservedMenuItem.addActionListener(new java.awt.event.ActionListener() - { - public void actionPerformed(ActionEvent e) - { - showUnconservedMenuItem_actionPerformed(e); - } - }); + showNonconservedMenuItem.setText("Show nonconserved"); + showNonconservedMenuItem.setState(false); + showNonconservedMenuItem + .addActionListener(new java.awt.event.ActionListener() + { + public void actionPerformed(ActionEvent e) + { + showUnconservedMenuItem_actionPerformed(e); + } + }); sortPairwiseMenuItem.setText("by Pairwise Identity"); sortPairwiseMenuItem .addActionListener(new java.awt.event.ActionListener() @@ -673,13 +684,14 @@ public class GAlignFrame extends JInternalFrame } }); sortLengthMenuItem.setText("By Length"); - sortLengthMenuItem.addActionListener(new java.awt.event.ActionListener() - { - public void actionPerformed(ActionEvent e) - { - sortLengthMenuItem_actionPerformed(e); - } - }); + sortLengthMenuItem + .addActionListener(new java.awt.event.ActionListener() + { + public void actionPerformed(ActionEvent e) + { + sortLengthMenuItem_actionPerformed(e); + } + }); sortGroupMenuItem.setText("by Group"); sortGroupMenuItem.addActionListener(new java.awt.event.ActionListener() { @@ -985,15 +997,12 @@ public class GAlignFrame extends JInternalFrame showSeqFeatures_actionPerformed(actionEvent); } }); -/* - * showSeqFeaturesHeight.setText("Vary Sequence Feature Height"); - showSeqFeaturesHeight.addActionListener(new ActionListener() - { - public void actionPerformed(ActionEvent actionEvent) - { - showSeqFeaturesHeight_actionPerformed(actionEvent); - } - }); */ + /* + * showSeqFeaturesHeight.setText("Vary Sequence Feature Height"); + * showSeqFeaturesHeight.addActionListener(new ActionListener() { public + * void actionPerformed(ActionEvent actionEvent) { + * showSeqFeaturesHeight_actionPerformed(actionEvent); } }); + */ showDbRefsMenuitem.setText("Show Database Refs"); showDbRefsMenuitem.addActionListener(new ActionListener() { @@ -1002,7 +1011,7 @@ public class GAlignFrame extends JInternalFrame { showDbRefs_actionPerformed(e); } - + }); showNpFeatsMenuitem.setText("Show Non-Positional Features"); showNpFeatsMenuitem.addActionListener(new ActionListener() @@ -1012,7 +1021,7 @@ public class GAlignFrame extends JInternalFrame { showNpFeats_actionPerformed(e); } - + }); showGroupConservation.setText("Group Conservation"); showGroupConservation.addActionListener(new ActionListener() @@ -1022,7 +1031,7 @@ public class GAlignFrame extends JInternalFrame { showGroupConservation_actionPerformed(e); } - + }); showGroupConsensus.setText("Group Consensus"); @@ -1033,7 +1042,7 @@ public class GAlignFrame extends JInternalFrame { showGroupConsensus_actionPerformed(e); } - + }); showConsensusHistogram.setText("Show Consensus Histogram"); showConsensusHistogram.addActionListener(new ActionListener() @@ -1043,7 +1052,7 @@ public class GAlignFrame extends JInternalFrame { showConsensusHistogram_actionPerformed(e); } - + }); showSequenceLogo.setText("Show Consensus Logo"); showSequenceLogo.addActionListener(new ActionListener() @@ -1053,7 +1062,7 @@ public class GAlignFrame extends JInternalFrame { showSequenceLogo_actionPerformed(e); } - + }); applyAutoAnnotationSettings.setText("Apply to all groups"); applyAutoAnnotationSettings.setState(false); @@ -1065,7 +1074,7 @@ public class GAlignFrame extends JInternalFrame { applyAutoAnnotationSettings_actionPerformed(e); } - + }); nucleotideColour.setText("Nucleotide"); @@ -1246,9 +1255,9 @@ public class GAlignFrame extends JInternalFrame { followHighlight_actionPerformed(); } - + }); - + modifyPID.setText("Modify Identity Threshold..."); modifyPID.addActionListener(new java.awt.event.ActionListener() { @@ -1342,7 +1351,7 @@ public class GAlignFrame extends JInternalFrame } }); extractScores.setVisible(true); // JBPNote: TODO: make gui for regex based - // score extraction + // score extraction showProducts.setText("Get Cross References"); /* * showProducts.addActionListener(new ActionListener() { @@ -1482,7 +1491,7 @@ public class GAlignFrame extends JInternalFrame } }); // TODO: should be hidden if no selection exists. - hideAllButSelection.setText("All but Selected Rregion (Shift+Ctrl+H)"); + hideAllButSelection.setText("All but Selected Region (Shift+Ctrl+H)"); hideAllButSelection.addActionListener(new ActionListener() { public void actionPerformed(ActionEvent e) @@ -1491,7 +1500,8 @@ public class GAlignFrame extends JInternalFrame } }); showAllhidden.setText("All Sequences and Columns"); - showAllhidden.setToolTipText("H toggles visibility of hidden or selected regions."); + showAllhidden + .setToolTipText("H toggles visibility of hidden or selected regions."); showAllhidden.addActionListener(new ActionListener() { public void actionPerformed(ActionEvent e) @@ -1697,8 +1707,8 @@ public class GAlignFrame extends JInternalFrame viewMenu.add(autoAnnMenu); viewMenu.addSeparator(); viewMenu.add(showSeqFeatures); - //viewMenu.add(showSeqFeaturesHeight); - + // viewMenu.add(showSeqFeaturesHeight); + viewMenu.add(featureSettings); tooltipSettingsMenu.add(showDbRefsMenuitem); tooltipSettingsMenu.add(showNpFeatsMenuitem); @@ -1769,7 +1779,7 @@ public class GAlignFrame extends JInternalFrame hideMenu.add(hideSelSequences); hideMenu.add(hideAllSelection); hideMenu.add(hideAllButSelection); - + formatMenu.add(font); formatMenu.addSeparator(); formatMenu.add(wrapMenuItem); @@ -1784,7 +1794,7 @@ public class GAlignFrame extends JInternalFrame formatMenu.add(colourTextMenuItem); formatMenu.add(renderGapsMenuItem); formatMenu.add(centreColumnLabelsMenuItem); - formatMenu.add(showUnconservedMenuItem); + formatMenu.add(showNonconservedMenuItem); selectMenu.add(findMenuItem); selectMenu.addSeparator(); selectMenu.add(selectAllSequenceMenuItem); @@ -1798,98 +1808,98 @@ public class GAlignFrame extends JInternalFrame protected void showAllhidden_actionPerformed(ActionEvent e) { // TODO Auto-generated method stub - + } protected void hideAllButSelection_actionPerformed(ActionEvent e) { // TODO Auto-generated method stub - + } protected void hideAllSelection_actionPerformed(ActionEvent e) { // TODO Auto-generated method stub - + } protected void applyAutoAnnotationSettings_actionPerformed(ActionEvent e) { // TODO Auto-generated method stub - + } protected void showConsensusHistogram_actionPerformed(ActionEvent e) { // TODO Auto-generated method stub - + } protected void showSequenceLogo_actionPerformed(ActionEvent e) { // TODO Auto-generated method stub - + } protected void makeGrpsFromSelection_actionPerformed(ActionEvent e) { // TODO Auto-generated method stub - + } protected void showGroupConsensus_actionPerformed(ActionEvent e) { // TODO Auto-generated method stub - + } protected void showGroupConservation_actionPerformed(ActionEvent e) { // TODO Auto-generated method stub - + } protected void showUnconservedMenuItem_actionPerformed(ActionEvent e) { // TODO Auto-generated method stub - + } protected void showSeqFeaturesHeight_actionPerformed( ActionEvent actionEvent) { // TODO Auto-generated method stub - + } protected void justifyRightMenuItem_actionPerformed(ActionEvent e) { // TODO Auto-generated method stub - + } protected void justifyLeftMenuItem_actionPerformed(ActionEvent e) { // TODO Auto-generated method stub - + } protected void followHighlight_actionPerformed() { // TODO Auto-generated method stub - + } protected void showNpFeats_actionPerformed(ActionEvent e) { // TODO Auto-generated method stub - + } protected void showDbRefs_actionPerformed(ActionEvent e) { // TODO Auto-generated method stub - + } protected void centreColumnLabels_actionPerformed(ActionEvent e)