X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FFeatureSettings.java;h=35690a95f2425796561d25b91b32dc9140f5fdd2;hb=e826112670b160df06adb4030835624248ac4a8a;hp=8c156624c3094166f1210b1b2b3f541e4ed3fcc7;hpb=c1d578127a42ebd8535c3135241e9b0da789d584;p=jalview.git diff --git a/src/jalview/gui/FeatureSettings.java b/src/jalview/gui/FeatureSettings.java index 8c15662..35690a9 100755 --- a/src/jalview/gui/FeatureSettings.java +++ b/src/jalview/gui/FeatureSettings.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5) - * Copyright (C) 2010 J Procter, AM Waterhouse, 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 file is part of Jalview. * @@ -19,11 +19,10 @@ 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 +37,7 @@ 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 { @@ -163,17 +163,24 @@ public class FeatureSettings extends JPanel frame = new JInternalFrame(); frame.setContentPane(this); - 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; - }; - }); + if (new jalview.util.Platform().isAMac()) + { + Desktop.addInternalFrame(frame, "Sequence Feature Settings", 475, 480); + } + 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); } @@ -273,8 +280,9 @@ 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); } } } @@ -305,15 +313,15 @@ 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() + 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; @@ -398,8 +406,8 @@ 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) { @@ -434,10 +442,10 @@ 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) { @@ -513,8 +521,8 @@ 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); } @@ -588,10 +596,10 @@ 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"); @@ -628,8 +636,8 @@ 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()); @@ -652,13 +660,11 @@ 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); @@ -688,10 +694,10 @@ 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"); @@ -898,7 +904,7 @@ 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() { @@ -907,7 +913,7 @@ 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() { @@ -916,7 +922,7 @@ 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() { @@ -925,7 +931,7 @@ 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() { @@ -934,7 +940,7 @@ 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() { @@ -944,7 +950,7 @@ 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() { @@ -953,7 +959,7 @@ 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() { @@ -962,7 +968,7 @@ 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() { @@ -1171,7 +1177,7 @@ 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; @@ -1219,9 +1225,9 @@ 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); } /** @@ -1247,14 +1253,14 @@ 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() @@ -1288,7 +1294,7 @@ public class FeatureSettings extends JPanel fetchDAS.setEnabled(true); cancelDAS.setEnabled(false); dassourceBrowser.setGuiEnabled(true); - + } public void cancelDAS_actionPerformed(ActionEvent e)