X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FFeatureSettings.java;h=9f73873b8662a0fccd3310f140f6c495fde370f5;hb=865a855a4ca87eadb3e5ff284ed32ed307d9c34b;hp=2139da5b2e2f7a537aa037d5cd1349a7a1a61df7;hpb=153dd62dc91da13ae732600e6ea55ddbe15eab39;p=jalview.git diff --git a/src/jalview/gui/FeatureSettings.java b/src/jalview/gui/FeatureSettings.java index 2139da5..9f73873 100755 --- a/src/jalview/gui/FeatureSettings.java +++ b/src/jalview/gui/FeatureSettings.java @@ -1,29 +1,29 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6) - * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1) + * Copyright (C) 2014 The Jalview Authors * * This file is part of Jalview. * * Jalview is free software: you can redistribute it and/or * modify it under the terms of the GNU General Public License * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. - * + * * 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 . + * The Jalview Authors are detailed in the 'AUTHORS' file. */ package jalview.gui; import java.io.*; import java.util.*; +import java.util.List; import java.awt.*; import java.awt.event.*; -import java.awt.geom.AffineTransform; -import java.awt.image.BufferedImage; import java.beans.PropertyChangeEvent; import java.beans.PropertyChangeListener; @@ -38,6 +38,7 @@ import jalview.datamodel.*; import jalview.io.*; import jalview.schemes.AnnotationColourGradient; import jalview.schemes.GraduatedColor; +import jalview.ws.dbsources.das.api.jalviewSourceI; public class FeatureSettings extends JPanel { @@ -165,21 +166,22 @@ public class FeatureSettings extends JPanel frame.setContentPane(this); if (new jalview.util.Platform().isAMac()) { - Desktop.addInternalFrame(frame, "Sequence Feature Settings", 475, 480); - } else { - Desktop.addInternalFrame(frame, "Sequence Feature Settings", 400, 450); + Desktop.addInternalFrame(frame, "Sequence Feature Settings", 475, 480); } - - frame - .addInternalFrameListener(new javax.swing.event.InternalFrameAdapter() - { - public void internalFrameClosed( - javax.swing.event.InternalFrameEvent evt) - { - fr.removePropertyChangeListener(change); - dassourceBrowser.fs = null; - }; - }); + else + { + Desktop.addInternalFrame(frame, "Sequence Feature Settings", 400, 450); + } + + frame.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter() + { + public void internalFrameClosed( + javax.swing.event.InternalFrameEvent evt) + { + fr.removePropertyChangeListener(change); + dassourceBrowser.fs = null; + }; + }); frame.setLayer(JLayeredPane.PALETTE_LAYER); } @@ -279,8 +281,9 @@ public class FeatureSettings extends JPanel // probably the color chooser! table.setValueAt(colorChooser.getColor(), selectedRow, 1); table.validate(); - me.updateFeatureRenderer(((FeatureTableModel) table - .getModel()).getData(), false); + me.updateFeatureRenderer( + ((FeatureTableModel) table.getModel()).getData(), + false); } } } @@ -311,15 +314,15 @@ public class FeatureSettings extends JPanel Vector allGroups = new Vector(); SequenceFeature[] tmpfeatures; String group; - for (int i = 0; i < af.getViewport().alignment.getHeight(); i++) + for (int i = 0; i < af.getViewport().getAlignment().getHeight(); i++) { - if (af.getViewport().alignment.getSequenceAt(i).getDatasetSequence() - .getSequenceFeatures() == null) + if (af.getViewport().getAlignment().getSequenceAt(i) + .getDatasetSequence().getSequenceFeatures() == null) { continue; } - tmpfeatures = af.getViewport().alignment.getSequenceAt(i) + tmpfeatures = af.getViewport().getAlignment().getSequenceAt(i) .getDatasetSequence().getSequenceFeatures(); int index = 0; @@ -404,8 +407,8 @@ public class FeatureSettings extends JPanel { public void itemStateChanged(ItemEvent evt) { - fr.featureGroups.put(check.getText(), new Boolean(check - .isSelected())); + fr.featureGroups.put(check.getText(), + new Boolean(check.isSelected())); af.alignPanel.seqPanel.seqCanvas.repaint(); if (af.alignPanel.overviewPanel != null) { @@ -440,10 +443,10 @@ public class FeatureSettings extends JPanel // Find out which features should be visible depending on which groups // are selected / deselected // and recompute average width ordering - for (int i = 0; i < af.getViewport().alignment.getHeight(); i++) + for (int i = 0; i < af.getViewport().getAlignment().getHeight(); i++) { - tmpfeatures = af.getViewport().alignment.getSequenceAt(i) + tmpfeatures = af.getViewport().getAlignment().getSequenceAt(i) .getDatasetSequence().getSequenceFeatures(); if (tmpfeatures == null) { @@ -519,8 +522,8 @@ public class FeatureSettings extends JPanel data[dataIndex][0] = type; data[dataIndex][1] = fr.getFeatureStyle(type); - data[dataIndex][2] = new Boolean(af.getViewport().featuresDisplayed - .containsKey(type)); + data[dataIndex][2] = new Boolean( + af.getViewport().featuresDisplayed.containsKey(type)); dataIndex++; visibleChecks.removeElement(type); } @@ -594,10 +597,10 @@ public class FeatureSettings extends JPanel void load() { - JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache - .getProperty("LAST_DIRECTORY"), new String[] - { "fc" }, new String[] - { "Sequence Feature Colours" }, "Sequence Feature Colours"); + JalviewFileChooser chooser = new JalviewFileChooser( + jalview.bin.Cache.getProperty("LAST_DIRECTORY"), new String[] + { "fc" }, new String[] + { "Sequence Feature Colours" }, "Sequence Feature Colours"); chooser.setFileView(new jalview.io.JalviewFileView()); chooser.setDialogTitle("Load Feature Colours"); chooser.setToolTipText("Load"); @@ -634,8 +637,8 @@ public class FeatureSettings extends JPanel Cache.log.warn("Couldn't parse out graduated feature color.", e); } - GraduatedColor gcol = new GraduatedColor(mincol, maxcol, newcol - .getMin(), newcol.getMax()); + GraduatedColor gcol = new GraduatedColor(mincol, maxcol, + newcol.getMin(), newcol.getMax()); if (newcol.hasAutoScale()) { gcol.setAutoScaled(newcol.getAutoScale()); @@ -658,13 +661,11 @@ public class FeatureSettings extends JPanel } if (ttyp.equalsIgnoreCase("ABOVE")) { - gcol - .setThreshType(AnnotationColourGradient.ABOVE_THRESHOLD); + gcol.setThreshType(AnnotationColourGradient.ABOVE_THRESHOLD); } if (ttyp.equalsIgnoreCase("BELOW")) { - gcol - .setThreshType(AnnotationColourGradient.BELOW_THRESHOLD); + gcol.setThreshType(AnnotationColourGradient.BELOW_THRESHOLD); } } fr.setColour(name = newcol.getName(), gcol); @@ -694,10 +695,10 @@ public class FeatureSettings extends JPanel void save() { - JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache - .getProperty("LAST_DIRECTORY"), new String[] - { "fc" }, new String[] - { "Sequence Feature Colours" }, "Sequence Feature Colours"); + JalviewFileChooser chooser = new JalviewFileChooser( + jalview.bin.Cache.getProperty("LAST_DIRECTORY"), new String[] + { "fc" }, new String[] + { "Sequence Feature Colours" }, "Sequence Feature Colours"); chooser.setFileView(new jalview.io.JalviewFileView()); chooser.setDialogTitle("Save Feature Colour Scheme"); chooser.setToolTipText("Save"); @@ -714,13 +715,13 @@ public class FeatureSettings extends JPanel PrintWriter out = new PrintWriter(new OutputStreamWriter( new FileOutputStream(choice), "UTF-8")); - Enumeration e = fr.featureColours.keys(); + Iterator e = fr.featureColours.keySet().iterator(); float[] sortOrder = new float[fr.featureColours.size()]; String[] sortTypes = new String[fr.featureColours.size()]; int i = 0; - while (e.hasMoreElements()) + while (e.hasNext()) { - sortTypes[i] = e.nextElement().toString(); + sortTypes[i] = e.next().toString(); sortOrder[i] = fr.getOrder(sortTypes[i]); i++; } @@ -904,7 +905,7 @@ public class FeatureSettings extends JPanel settingsPane.setLayout(borderLayout2); dasSettingsPane.setLayout(borderLayout3); bigPanel.setLayout(borderLayout4); - invert.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11)); + invert.setFont(JvSwingUtils.getLabelFont()); invert.setText("Invert Selection"); invert.addActionListener(new ActionListener() { @@ -913,7 +914,7 @@ public class FeatureSettings extends JPanel invertSelection(); } }); - optimizeOrder.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11)); + optimizeOrder.setFont(JvSwingUtils.getLabelFont()); optimizeOrder.setText("Optimise Order"); optimizeOrder.addActionListener(new ActionListener() { @@ -922,7 +923,7 @@ public class FeatureSettings extends JPanel orderByAvWidth(); } }); - sortByScore.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11)); + sortByScore.setFont(JvSwingUtils.getLabelFont()); sortByScore.setText("Seq sort by Score"); sortByScore.addActionListener(new ActionListener() { @@ -931,7 +932,7 @@ public class FeatureSettings extends JPanel sortByScore(null); } }); - sortByDens.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11)); + sortByDens.setFont(JvSwingUtils.getLabelFont()); sortByDens.setText("Seq Sort by density"); sortByDens.addActionListener(new ActionListener() { @@ -940,7 +941,7 @@ public class FeatureSettings extends JPanel sortByDens(null); } }); - cancel.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11)); + cancel.setFont(JvSwingUtils.getLabelFont()); cancel.setText("Cancel"); cancel.addActionListener(new ActionListener() { @@ -950,7 +951,7 @@ public class FeatureSettings extends JPanel close(); } }); - ok.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11)); + ok.setFont(JvSwingUtils.getLabelFont()); ok.setText("OK"); ok.addActionListener(new ActionListener() { @@ -959,7 +960,7 @@ public class FeatureSettings extends JPanel close(); } }); - loadColours.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11)); + loadColours.setFont(JvSwingUtils.getLabelFont()); loadColours.setText("Load Colours"); loadColours.addActionListener(new ActionListener() { @@ -968,7 +969,7 @@ public class FeatureSettings extends JPanel load(); } }); - saveColours.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11)); + saveColours.setFont(JvSwingUtils.getLabelFont()); saveColours.setText("Save Colours"); saveColours.addActionListener(new ActionListener() { @@ -1134,13 +1135,13 @@ public class FeatureSettings extends JPanel if (fr.featureGroups != null) { - Enumeration en = fr.featureGroups.keys(); + Iterator en = fr.featureGroups.keySet().iterator(); gps = new String[fr.featureColours.size()]; int g = 0; boolean valid = false; - while (en.hasMoreElements()) + while (en.hasNext()) { - String gp = (String) en.nextElement(); + String gp = (String) en.next(); Boolean on = (Boolean) fr.featureGroups.get(gp); if (on != null && on.booleanValue()) { @@ -1177,7 +1178,7 @@ public class FeatureSettings extends JPanel * @param checkDbRefs * @param promptFetchDbRefs */ - private void doDasFeatureFetch(Vector selectedSources, + private void doDasFeatureFetch(List selectedSources, boolean checkDbRefs, boolean promptFetchDbRefs) { SequenceI[] dataset, seqs; @@ -1225,9 +1226,9 @@ public class FeatureSettings extends JPanel * Vector of Strings to resolve to DAS source nicknames. * @return sources that are present in source list. */ - public Vector resolveSourceNicknames(Vector sources) + public List resolveSourceNicknames(Vector sources) { - return dassourceBrowser.resolveSourceNicknames(sources); + return dassourceBrowser.sourceRegistry.resolveSourceNicknames(sources); } /** @@ -1253,14 +1254,15 @@ public class FeatureSettings extends JPanel public void fetchDasFeatures(Vector sources, boolean block) { initDasSources(); - Vector resolved = resolveSourceNicknames(sources); + List resolved = dassourceBrowser.sourceRegistry + .resolveSourceNicknames(sources); if (resolved.size() == 0) { resolved = dassourceBrowser.getSelectedSources(); } if (resolved.size() > 0) { - final Vector dassources = resolved; + final List dassources = resolved; fetchDAS.setEnabled(false); // cancelDAS.setEnabled(true); doDasFetch does this. Runnable fetcher = new Runnable() @@ -1294,7 +1296,7 @@ public class FeatureSettings extends JPanel fetchDAS.setEnabled(true); cancelDAS.setEnabled(false); dassourceBrowser.setGuiEnabled(true); - + } public void cancelDAS_actionPerformed(ActionEvent e)