X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FFeatureSettings.java;h=e137416b421cb9b2161a0842fbac2b3225769e75;hb=a45774ee31d9f35d4eff46d54d7deab719afb092;hp=f71159dcfdd4fd364ba2495df9cfa07393c3aa9d;hpb=d2e7e2612a39826b30cf92889441ce99b36e7a40;p=jalview.git diff --git a/src/jalview/appletgui/FeatureSettings.java b/src/jalview/appletgui/FeatureSettings.java index f71159d..e137416 100755 --- a/src/jalview/appletgui/FeatureSettings.java +++ b/src/jalview/appletgui/FeatureSettings.java @@ -1,20 +1,19 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4) - * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7) + * Copyright (C) 2011 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; @@ -26,6 +25,8 @@ import java.awt.event.*; import jalview.analysis.AlignmentSorter; import jalview.commands.OrderCommand; import jalview.datamodel.*; +import jalview.schemes.AnnotationColourGradient; +import jalview.schemes.GraduatedColor; public class FeatureSettings extends Panel implements ItemListener, MouseListener, MouseMotionListener, ActionListener, @@ -154,9 +155,12 @@ public class FeatureSettings extends Panel implements ItemListener, g.drawString("(Features can be added from searches or", 10, 40); g.drawString("from Jalview / GFF features files)", 10, 60); } - protected void popupSort(final String type, final Hashtable minmax, + + protected void popupSort(final MyCheckbox check, final Hashtable minmax, int x, int y) { + final String type = check.type; + final Object typeCol = fr.getFeatureStyle(type); java.awt.PopupMenu men = new PopupMenu("Settings for " + type); java.awt.MenuItem scr = new MenuItem("Sort by Score"); men.add(scr); @@ -186,38 +190,42 @@ public class FeatureSettings extends Panel implements ItemListener, if (minmax != null) { final Object typeMinMax = minmax.get(type); - final java.awt.CheckboxMenuItem chb = new java.awt.CheckboxMenuItem("Vary Height"); - // this is broken at the moment - chb.setState(minmax.get(type) != null); - chb.addActionListener(new ActionListener() - { - - public void actionPerformed(ActionEvent e) - { - chb.setState(chb.getState()); - if (chb.getState()) - { - minmax.put(type, null); - } - else - { - minmax.put(type, typeMinMax); - } - } - - }); - men.add(chb); + /* + * final java.awt.CheckboxMenuItem chb = new + * java.awt.CheckboxMenuItem("Vary Height"); // this is broken at the + * moment chb.setState(minmax.get(type) != null); + * chb.addActionListener(new ActionListener() { + * + * public void actionPerformed(ActionEvent e) { + * chb.setState(chb.getState()); if (chb.getState()) { minmax.put(type, + * null); } else { minmax.put(type, typeMinMax); } } + * + * }); men.add(chb); + */ if (typeMinMax != null && ((float[][]) typeMinMax)[0] != null) { - // graduated colourschemes for those where minmax exists for the positional features - MenuItem mxcol = new MenuItem("Min Max Colour"); + // graduated colourschemes for those where minmax exists for the + // positional features + 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); + 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)); + } } }); @@ -309,14 +317,14 @@ public class FeatureSettings extends Panel implements ItemListener, Component[] comps; int cSize = featurePanel.getComponentCount(); - Checkbox check; + MyCheckbox check; // This will remove any checkboxes which shouldn't be // visible for (int i = 0; i < cSize; i++) { comps = featurePanel.getComponents(); - check = (Checkbox) comps[i]; - if (!visibleChecks.contains(check.getLabel())) + check = (MyCheckbox) comps[i]; + if (!visibleChecks.contains(check.type)) { featurePanel.remove(i); cSize--; @@ -368,21 +376,21 @@ public class FeatureSettings extends Panel implements ItemListener, * update the checklist of feature types with the given type * * @param groupsChanged - * true means if the type is not in the display list then it - * will be added and displayed + * true means if the type is not in the display list then it will be + * added and displayed * @param type - * feature type to be checked for in the list. + * feature type to be checked for in the list. */ void addCheck(boolean groupsChanged, String type) { boolean addCheck; Component[] comps = featurePanel.getComponents(); - Checkbox check; + MyCheckbox check; addCheck = true; for (int i = 0; i < featurePanel.getComponentCount(); i++) { - check = (Checkbox) comps[i]; - if (check.getLabel().equals(type)) + check = (MyCheckbox) comps[i]; + if (check.type.equals(type)) { addCheck = false; break; @@ -400,11 +408,11 @@ public class FeatureSettings extends Panel implements ItemListener, check = new MyCheckbox( type, selected, - (fr.featureLinks != null && fr.featureLinks.containsKey(type))); + (fr.featureLinks != null && fr.featureLinks.containsKey(type)), + fr.getFeatureStyle(type)); check.addMouseListener(this); check.addMouseMotionListener(this); - check.setBackground(fr.getColour(type)); check.addItemListener(this); if (groupsChanged) { @@ -437,8 +445,8 @@ 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) { @@ -461,9 +469,9 @@ public class FeatureSettings extends Panel implements ItemListener, int tmpSize = 0; for (int i = 0; i < cSize; i++) { - Checkbox check = (Checkbox) comps[i]; - tmp[tmpSize][0] = check.getLabel(); - tmp[tmpSize][1] = fr.getColour(check.getLabel()); + MyCheckbox check = (MyCheckbox) comps[i]; + tmp[tmpSize][0] = check.type; + tmp[tmpSize][1] = fr.getFeatureStyle(check.type); tmp[tmpSize][2] = new Boolean(check.getState()); tmpSize++; } @@ -486,7 +494,7 @@ public class FeatureSettings extends Panel implements ItemListener, selectedCheck = (MyCheckbox) evt.getSource(); if (fr.featureLinks != null - && fr.featureLinks.containsKey(selectedCheck.getLabel())) + && fr.featureLinks.containsKey(selectedCheck.type)) { if (evt.getX() > selectedCheck.stringWidth + 20) { @@ -557,9 +565,23 @@ 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( + "Implementation error: Unsupported feature colour object."); + } + refreshTable(); + } + + public void refreshTable() { - fr.setColour(feature, col); featurePanel.removeAll(); resetTable(false); ap.paintAlignment(true); @@ -576,19 +598,18 @@ public class FeatureSettings extends Panel implements ItemListener, public void mouseClicked(MouseEvent evt) { MyCheckbox check = (MyCheckbox) evt.getSource(); - if ((evt.getModifiers() & InputEvent.BUTTON3_MASK)!=0) + if ((evt.getModifiers() & InputEvent.BUTTON3_MASK) != 0) { - this.popupSort(check.getLabel(), fr.minmax, evt.getX(), evt.getY()); + this.popupSort(check, fr.minmax, evt.getX(), evt.getY()); } - if (fr.featureLinks != null - && fr.featureLinks.containsKey(check.getLabel())) + if (fr.featureLinks != null && fr.featureLinks.containsKey(check.type)) { if (evt.getX() > check.stringWidth + 20) { evt.consume(); - String link = fr.featureLinks.get(check.getLabel()).toString(); - ap.alignFrame.showURL(link.substring(link.indexOf("|") + 1), link - .substring(0, link.indexOf("|"))); + String link = fr.featureLinks.get(check.type).toString(); + ap.alignFrame.showURL(link.substring(link.indexOf("|") + 1), + link.substring(0, link.indexOf("|"))); } } @@ -599,8 +620,17 @@ public class FeatureSettings extends Panel implements ItemListener, if (evt.getClickCount() > 1) { - new UserDefinedColours(this, check.getLabel(), fr.getColour(check - .getLabel())); + Object fcol = fr.getFeatureStyle(check.type); + if (fcol instanceof Color) + { + new UserDefinedColours(this, check.type, (Color) fcol); + } + else + { + new FeatureColourChooser(this, check.type); + // write back the current colour object to update the table + check.updateColor(fr.getFeatureStyle(check.type)); + } } } @@ -617,21 +647,105 @@ public class FeatureSettings extends Panel implements ItemListener, class MyCheckbox extends Checkbox { + public String type; + public int stringWidth; boolean hasLink; + GraduatedColor gcol; + + Color col; + + public void updateColor(Object newcol) + { + if (newcol instanceof Color) + { + col = (Color) newcol; + gcol = null; + } + else if (newcol instanceof GraduatedColor) + { + gcol = (GraduatedColor) newcol; + col = null; + } + else + { + throw new Error("Invalid color for MyCheckBox"); + } + if (col != null) + { + setBackground(col); + } + else + { + String vlabel = type; + if (gcol.getThreshType() != AnnotationColourGradient.NO_THRESHOLD) + { + vlabel += " " + + ((gcol.getThreshType() == AnnotationColourGradient.ABOVE_THRESHOLD) ? "(>)" + : "(<)"); + } + if (gcol.isColourByLabel()) + { + setBackground(Color.white); + vlabel += " (by Label)"; + } + else + { + setBackground(gcol.getMinColor()); + } + this.setLabel(vlabel); + } + repaint(); + } + public MyCheckbox(String label, boolean checked, boolean haslink) { super(label, checked); - + type = label; FontMetrics fm = av.nullFrame.getFontMetrics(av.nullFrame.getFont()); stringWidth = fm.stringWidth(label); this.hasLink = haslink; } + public MyCheckbox(String type, boolean selected, boolean b, + Object featureStyle) + { + this(type, selected, b); + updateColor(featureStyle); + } + public void paint(Graphics g) { + Dimension d = getSize(); + if (gcol != null) + { + if (gcol.isColourByLabel()) + { + g.setColor(Color.white); + 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(d.width / 2, 0, d.width / 2, d.height); + + } + } + if (hasLink) { g.drawImage(linkImage, stringWidth + 25, @@ -639,10 +753,12 @@ public class FeatureSettings extends Panel implements ItemListener, } } } + protected void sortByDens(String[] typ) { sortBy(typ, "Sort by Density", AlignmentSorter.FEATURE_DENSITY); } + private String[] getDisplayedFeatureTypes() { String[] typ = null; @@ -664,7 +780,6 @@ public class FeatureSettings extends Panel implements ItemListener, return typ; } - protected void sortBy(String[] typ, String methodText, final String method) { if (typ == null) @@ -705,8 +820,8 @@ public class FeatureSettings extends Panel implements ItemListener, } SequenceI[] oldOrder = al.getSequencesArray(); AlignmentSorter.sortByFeature(typ, gps, start, stop, al, method); - this.ap.alignFrame.addHistoryItem(new OrderCommand(methodText, oldOrder, alignPanel.av - .getAlignment())); + this.ap.alignFrame.addHistoryItem(new OrderCommand(methodText, + oldOrder, alignPanel.av.getAlignment())); alignPanel.paintAlignment(true); }