X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FFeatureSettings.java;h=39c984db7a4d7d3cc3001fab59618792b825ebc0;hb=ab43013b7e357b84b4abade0dba949668dfb2a0e;hp=80559bd94c76ec6f94ce07dd9a2c53f34a512adf;hpb=262352d44a49e6102a9e80b0c006ea9331ed0c67;p=jalview.git diff --git a/src/jalview/appletgui/FeatureSettings.java b/src/jalview/appletgui/FeatureSettings.java index 80559bd..39c984d 100755 --- a/src/jalview/appletgui/FeatureSettings.java +++ b/src/jalview/appletgui/FeatureSettings.java @@ -1,20 +1,22 @@ /* - * 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 2.8.2b1) + * Copyright (C) 2014 The Jalview Authors * - * 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. + * + * 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 + * along with Jalview. If not, see . + * The Jalview Authors are detailed in the 'AUTHORS' file. */ package jalview.appletgui; @@ -28,6 +30,7 @@ import jalview.commands.OrderCommand; import jalview.datamodel.*; import jalview.schemes.AnnotationColourGradient; import jalview.schemes.GraduatedColor; +import jalview.util.MessageManager; public class FeatureSettings extends Panel implements ItemListener, MouseListener, MouseMotionListener, ActionListener, @@ -119,8 +122,10 @@ public class FeatureSettings extends Panel implements ItemListener, if (groupPanel != null) { - groupPanel.setLayout(new GridLayout(fr.featureGroups.size() / 4 + 1, - 4)); + groupPanel + .setLayout(new GridLayout( + (fr.featureGroups.size() - fr.hiddenGroups.size()) / 4 + 1, + 4)); groupPanel.validate(); add(groupPanel, BorderLayout.NORTH); @@ -145,24 +150,34 @@ public class FeatureSettings extends Panel implements ItemListener, height = Math.max(200, height); height = Math.min(400, height); int width = 300; - jalview.bin.JalviewLite.addFrame(frame, "Feature Settings", width, + jalview.bin.JalviewLite.addFrame(frame, + MessageManager.getString("label.feature_settings"), width, height); } public void paint(Graphics g) { g.setColor(Color.black); - g.drawString("No Features added to this alignment!!", 10, 20); - g.drawString("(Features can be added from searches or", 10, 40); - g.drawString("from Jalview / GFF features files)", 10, 60); + g.drawString(MessageManager + .getString("label.no_features_added_to_this_alignment"), 10, 20); + g.drawString(MessageManager + .getString("label.features_can_be_added_from_searches_1"), 10, + 40); + g.drawString(MessageManager + .getString("label.features_can_be_added_from_searches_2"), 10, + 60); } protected void popupSort(final MyCheckbox check, final Hashtable minmax, int x, int y) { final String type = check.type; - java.awt.PopupMenu men = new PopupMenu("Settings for " + type); - java.awt.MenuItem scr = new MenuItem("Sort by Score"); + final Object typeCol = fr.getFeatureStyle(type); + java.awt.PopupMenu men = new PopupMenu(MessageManager.formatMessage( + "label.settings_for_type", new String[] + { type })); + java.awt.MenuItem scr = new MenuItem( + MessageManager.getString("label.sort_by_score")); men.add(scr); final FeatureSettings me = this; scr.addActionListener(new ActionListener() @@ -175,7 +190,8 @@ public class FeatureSettings extends Panel implements ItemListener, } }); - MenuItem dens = new MenuItem("Sort by Density"); + MenuItem dens = new MenuItem( + MessageManager.getString("label.sort_by_density")); dens.addActionListener(new ActionListener() { @@ -206,16 +222,26 @@ public class FeatureSettings extends Panel implements ItemListener, { // graduated colourschemes for those where minmax exists for the // positional features - MenuItem mxcol = new MenuItem("Graduated Colour"); + MenuItem mxcol = new MenuItem( + (typeCol instanceof Color) ? "Graduated Colour" + : "Single Colour"); men.add(mxcol); mxcol.addActionListener(new ActionListener() { public void actionPerformed(ActionEvent e) { - new FeatureColourChooser(me, type); - // write back the current colour object to update the table - check.updateColor(fr.getFeatureStyle(type)); + if (typeCol instanceof Color) + { + new FeatureColourChooser(me, type); + // write back the current colour object to update the table + check.updateColor(fr.getFeatureStyle(type)); + } + else + { + new UserDefinedColours(me, check.type, + ((GraduatedColor) typeCol)); + } } }); @@ -251,7 +277,8 @@ public class FeatureSettings extends Panel implements ItemListener, rdrw = true; groupPanel.removeAll(); } - + // TODO: JAL-964 - smoothly incorporate new group entries if panel already + // displayed and new groups present Enumeration gps = fr.featureGroups.keys(); while (gps.hasMoreElements()) { @@ -263,6 +290,7 @@ public class FeatureSettings extends Panel implements ItemListener, check.addMouseListener(this); check.setFont(new Font("Serif", Font.BOLD, 12)); check.addItemListener(this); + check.setVisible(fr.hiddenGroups.contains(group)); groupPanel.add(check); } if (rdrw) @@ -278,15 +306,15 @@ public class FeatureSettings extends Panel implements ItemListener, SequenceFeature[] tmpfeatures; String group = null, type; Vector visibleChecks = new Vector(); - - for (int i = 0; i < av.alignment.getHeight(); i++) + AlignmentI alignment = av.getAlignment(); + for (int i = 0; i < alignment.getHeight(); i++) { - if (av.alignment.getSequenceAt(i).getSequenceFeatures() == null) + if (alignment.getSequenceAt(i).getSequenceFeatures() == null) { continue; } - tmpfeatures = av.alignment.getSequenceAt(i).getSequenceFeatures(); + tmpfeatures = alignment.getSequenceAt(i).getSequenceFeatures(); int index = 0; while (index < tmpfeatures.length) { @@ -435,8 +463,8 @@ public class FeatureSettings extends Panel implements ItemListener, Checkbox source = (Checkbox) evt.getSource(); if (fr.featureGroups.containsKey(source.getLabel())) { - fr.featureGroups.put(source.getLabel(), new Boolean(source - .getState())); + fr.featureGroups.put(source.getLabel(), + new Boolean(source.getState())); ap.seqPanel.seqCanvas.repaint(); if (ap.overviewPanel != null) { @@ -555,9 +583,22 @@ public class FeatureSettings extends Panel implements ItemListener, } } - public void setUserColour(String feature, Color col) + public void setUserColour(String feature, Object originalColour) + { + if (originalColour instanceof Color + || originalColour instanceof GraduatedColor) + { + fr.setColour(feature, originalColour); + } + else + { + throw new Error(MessageManager.getString("error.implementation_error_unsupported_feature_colour_object")); + } + refreshTable(); + } + + public void refreshTable() { - fr.setColour(feature, col); featurePanel.removeAll(); resetTable(false); ap.paintAlignment(true); @@ -578,15 +619,14 @@ public class FeatureSettings extends Panel implements ItemListener, { this.popupSort(check, fr.minmax, evt.getX(), evt.getY()); } - if (fr.featureLinks != null - && fr.featureLinks.containsKey(check.type)) + if (fr.featureLinks != null && fr.featureLinks.containsKey(check.type)) { if (evt.getX() > check.stringWidth + 20) { evt.consume(); String link = fr.featureLinks.get(check.type).toString(); - ap.alignFrame.showURL(link.substring(link.indexOf("|") + 1), link - .substring(0, link.indexOf("|"))); + ap.alignFrame.showURL(link.substring(link.indexOf("|") + 1), + link.substring(0, link.indexOf("|"))); } } @@ -601,7 +641,9 @@ public class FeatureSettings extends Panel implements ItemListener, if (fcol instanceof Color) { new UserDefinedColours(this, check.type, (Color) fcol); - } else { + } + else + { new FeatureColourChooser(this, check.type); // write back the current colour object to update the table check.updateColor(fr.getFeatureStyle(check.type)); @@ -623,6 +665,7 @@ public class FeatureSettings extends Panel implements ItemListener, class MyCheckbox extends Checkbox { public String type; + public int stringWidth; boolean hasLink; @@ -645,7 +688,7 @@ public class FeatureSettings extends Panel implements ItemListener, } else { - throw new Error("Invalid color for MyCheckBox"); + throw new Error(MessageManager.getString("error.invalid_colour_for_mycheckbox")); } if (col != null) { @@ -654,14 +697,19 @@ public class FeatureSettings extends Panel implements ItemListener, else { String vlabel = type; - if (gcol.getThreshType()!=AnnotationColourGradient.NO_THRESHOLD) + if (gcol.getThreshType() != AnnotationColourGradient.NO_THRESHOLD) { - vlabel += " "+((gcol.getThreshType()==AnnotationColourGradient.ABOVE_THRESHOLD) ? "(>)" : "(<)"); + vlabel += " " + + ((gcol.getThreshType() == AnnotationColourGradient.ABOVE_THRESHOLD) ? "(>)" + : "(<)"); } - if (gcol.isColourByLabel()) { + if (gcol.isColourByLabel()) + { setBackground(Color.white); vlabel += " (by Label)"; - } else { + } + else + { setBackground(gcol.getMinColor()); } this.setLabel(vlabel); @@ -681,36 +729,37 @@ public class FeatureSettings extends Panel implements ItemListener, public MyCheckbox(String type, boolean selected, boolean b, Object featureStyle) { - this(type,selected,b); + this(type, selected, b); updateColor(featureStyle); } public void paint(Graphics g) { - int width = getWidth(), height = getHeight(); + Dimension d = getSize(); if (gcol != null) { if (gcol.isColourByLabel()) { g.setColor(Color.white); - g.fillRect(width/2, 0,width/2, height); - /*g.setColor(Color.black); - Font f=g.getFont().deriveFont(9); - g.setFont(f); - - // g.setFont(g.getFont().deriveFont( - // AffineTransform.getScaleInstance( - // width/g.getFontMetrics().stringWidth("Label"), - // height/g.getFontMetrics().getHeight()))); - g.drawString("Label", width/2, 0); */ + g.fillRect(d.width / 2, 0, d.width / 2, d.height); + /* + * g.setColor(Color.black); Font f=g.getFont().deriveFont(9); + * g.setFont(f); + * + * // g.setFont(g.getFont().deriveFont( // + * AffineTransform.getScaleInstance( // + * width/g.getFontMetrics().stringWidth("Label"), // + * height/g.getFontMetrics().getHeight()))); g.drawString("Label", + * width/2, 0); + */ } else { Color maxCol = gcol.getMaxColor(); g.setColor(maxCol); - g.fillRect(width/2, 0,width/2, height); - + g.fillRect(d.width / 2, 0, d.width / 2, d.height); + } }