-/*\r
- * Jalview - A Sequence Alignment Editor and Viewer\r
- * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
- *\r
- * This program is free software; you can redistribute it and/or\r
- * modify it under the terms of the GNU General Public License\r
- * as published by the Free Software Foundation; either version 2\r
- * of the License, or (at your option) any later version.\r
- *\r
- * This program is distributed in the hope that it will be useful,\r
- * but WITHOUT ANY WARRANTY; without even the implied warranty of\r
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\r
- * GNU General Public License for more details.\r
- *\r
- * You should have received a copy of the GNU General Public License\r
- * along with this program; if not, write to the Free Software\r
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
- */\r
-package jalview.appletgui;\r
-\r
-import jalview.datamodel.*;\r
-import java.awt.*;\r
-import java.util.*;\r
-import java.awt.event.*;\r
-\r
-\r
-public class FeatureSettings extends Panel implements ItemListener,\r
- MouseListener, MouseMotionListener\r
-{\r
- final FeatureRenderer fr;\r
- final AlignmentPanel ap;\r
- final AlignViewport av;\r
- final Frame frame;\r
-\r
- public FeatureSettings(AlignViewport av, final AlignmentPanel ap)\r
- {\r
- this.ap = ap;\r
- this.av = av;\r
- fr = ap.seqPanel.seqCanvas.getFeatureRenderer();\r
-\r
- setTableData();\r
-\r
- frame = new Frame();\r
- frame.add(this);\r
- int height = this.getComponentCount()*50;\r
- if (height>400)\r
- height = 400;\r
-\r
- jalview.bin.JalviewLite.addFrame(frame, "Feature Settings", 200,\r
- height);\r
- }\r
-\r
- void setTableData()\r
- {\r
- Vector allFeatures = new Vector();\r
- Vector features;\r
- Enumeration e;\r
- SequenceFeature sf;\r
-\r
- for (int i = 0; i < av.alignment.getHeight(); i++)\r
- {\r
- features = av.alignment.getSequenceAt(i).getSequenceFeatures();\r
- if (features == null)\r
- continue;\r
-\r
- e = features.elements();\r
- while (e.hasMoreElements())\r
- {\r
- sf = (SequenceFeature) e.nextElement();\r
- if (!allFeatures.contains(sf.getType()))\r
- {\r
- allFeatures.addElement(sf.getType());\r
- }\r
- }\r
- }\r
-\r
- int fSize = allFeatures.size();\r
-\r
- String type;\r
- this.setLayout(new GridLayout(fSize, 2, 10,5));\r
-\r
- for (int i = 0; i < fSize; i++)\r
- {\r
- type = allFeatures.elementAt(i).toString();\r
- Color col = fr.getColour(type);\r
- boolean displayed = true;\r
- if(fr.featuresDisplayed!=null)\r
- displayed = fr.featuresDisplayed.contains(type);\r
-\r
- Checkbox check = new Checkbox(type, displayed);\r
- check.addMouseListener(this);\r
- check.addMouseMotionListener(this);\r
- check.setBackground(col);\r
- check.addItemListener(this);\r
- add(check);\r
- }\r
- validate();\r
- }\r
-\r
- public void itemStateChanged(ItemEvent evt)\r
- {\r
- Component [] comps = this.getComponents();\r
- int cSize = comps.length;\r
-\r
- Object [][] data = new Object[cSize][3];\r
-\r
- for(int i=0; i<cSize; i++)\r
- {\r
- Checkbox check = (Checkbox)comps[i];\r
- data[i][0] = check.getLabel();\r
- data[i][1] = fr.getColour(check.getLabel());\r
- data[i][2] = new Boolean(check.getState());\r
- }\r
-\r
- fr.setFeaturePriority(data);\r
- ap.seqPanel.seqCanvas.repaint();\r
- }\r
-\r
- Checkbox selectedCheck;\r
- boolean dragging = false;\r
-\r
- public void mousePressed(MouseEvent evt)\r
- {\r
- selectedCheck = (Checkbox)evt.getSource();\r
- }\r
-\r
- public void mouseDragged(MouseEvent evt)\r
- {\r
- dragging = true;\r
- }\r
-\r
- public void mouseReleased(MouseEvent evt)\r
- {\r
- Component comp = null;\r
- Checkbox target = null;\r
-\r
- int height = evt.getY()+evt.getComponent().getLocation().y;\r
-\r
- if(height > this.getSize().height)\r
- {\r
- comp = this.getComponent(this.getComponentCount()-1);\r
- }\r
- else if(height < 0)\r
- {\r
- comp = this.getComponent(0);\r
- }\r
- else\r
- {\r
- comp = this.getComponentAt(evt.getX(),\r
- evt.getY() +\r
- evt.getComponent().getLocation().y);\r
- }\r
-\r
- if(comp!=null && comp instanceof Checkbox)\r
- target = (Checkbox)comp;\r
-\r
- if (selectedCheck != null && target != null && selectedCheck != target)\r
- {\r
- int targetIndex = -1;\r
- for(int i=0; i<this.getComponentCount(); i++)\r
- {\r
- if(target==this.getComponent(i))\r
- { targetIndex = i; break; }\r
- }\r
-\r
-\r
- this.remove(selectedCheck);\r
- this.add(selectedCheck, targetIndex);\r
- validate();\r
- }\r
- }\r
-\r
-\r
- public void mouseEntered(MouseEvent evt){}\r
- public void mouseExited(MouseEvent evt){}\r
- public void mouseClicked(MouseEvent evt){}\r
- public void mouseMoved(MouseEvent evt){}\r
-}\r
+/*
+ * 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.
+ *
+ * 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 <http://www.gnu.org/licenses/>.
+ */
+package jalview.appletgui;
+
+import java.util.*;
+
+import java.awt.*;
+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,
+ AdjustmentListener
+{
+ FeatureRenderer fr;
+
+ AlignmentPanel ap;
+
+ AlignViewport av;
+
+ Frame frame;
+
+ Panel groupPanel;
+
+ Panel featurePanel = new Panel();
+
+ ScrollPane scrollPane;
+
+ boolean alignmentHasFeatures = false;
+
+ Image linkImage;
+
+ Scrollbar transparency;
+
+ public FeatureSettings(final AlignmentPanel ap)
+ {
+ this.ap = ap;
+ this.av = ap.av;
+ ap.av.featureSettings = this;
+ fr = ap.seqPanel.seqCanvas.getFeatureRenderer();
+
+ transparency = new Scrollbar(Scrollbar.HORIZONTAL,
+ 100 - (int) (fr.transparency * 100), 1, 1, 100);
+
+ if (fr.transparencySetter != null)
+ {
+ transparency.addAdjustmentListener(this);
+ }
+ else
+ {
+ transparency.setEnabled(false);
+ }
+
+ java.net.URL url = getClass().getResource("/images/link.gif");
+ if (url != null)
+ {
+ linkImage = java.awt.Toolkit.getDefaultToolkit().getImage(url);
+ }
+
+ if (av.featuresDisplayed == null)
+ {
+ fr.findAllFeatures();
+ }
+
+ setTableData();
+
+ this.setLayout(new BorderLayout());
+ scrollPane = new ScrollPane();
+ scrollPane.add(featurePanel);
+ if (alignmentHasFeatures)
+ {
+ add(scrollPane, BorderLayout.CENTER);
+ }
+
+ Button invert = new Button("Invert Selection");
+ invert.addActionListener(this);
+
+ Panel lowerPanel = new Panel(new GridLayout(2, 1, 5, 10));
+ lowerPanel.add(invert);
+
+ Panel tPanel = new Panel(new BorderLayout());
+
+ if (fr.transparencySetter != null)
+ {
+ tPanel.add(transparency, BorderLayout.CENTER);
+ tPanel.add(new Label("Transparency"), BorderLayout.EAST);
+ }
+ else
+ {
+ tPanel.add(
+ new Label("Transparency not available in this web browser"),
+ BorderLayout.CENTER);
+ }
+
+ lowerPanel.add(tPanel, BorderLayout.SOUTH);
+
+ add(lowerPanel, BorderLayout.SOUTH);
+
+ if (groupPanel != null)
+ {
+ groupPanel.setLayout(new GridLayout(fr.featureGroups.size() / 4 + 1,
+ 4));
+ groupPanel.validate();
+
+ add(groupPanel, BorderLayout.NORTH);
+ }
+ frame = new Frame();
+ frame.add(this);
+ final FeatureSettings me = this;
+ frame.addWindowListener(new WindowAdapter()
+ {
+ public void windowClosing(WindowEvent e)
+ {
+ if (me.av.featureSettings == me)
+ {
+ me.av.featureSettings = null;
+ me.ap = null;
+ me.av = null;
+ }
+ }
+ });
+ int height = featurePanel.getComponentCount() * 50 + 60;
+
+ height = Math.max(200, height);
+ height = Math.min(400, height);
+ int width = 300;
+ jalview.bin.JalviewLite.addFrame(frame, "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);
+ }
+
+ 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);
+ final FeatureSettings me = this;
+ scr.addActionListener(new ActionListener()
+ {
+
+ public void actionPerformed(ActionEvent e)
+ {
+ me.sortByScore(new String[]
+ { type });
+ }
+
+ });
+ MenuItem dens = new MenuItem("Sort by Density");
+ dens.addActionListener(new ActionListener()
+ {
+
+ public void actionPerformed(ActionEvent e)
+ {
+ me.sortByDens(new String[]
+ { type });
+ }
+
+ });
+ men.add(dens);
+ 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);
+ */
+ if (typeMinMax != null && ((float[][]) typeMinMax)[0] != null)
+ {
+ // 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)
+ {
+ 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));
+ }
+ }
+
+ });
+ }
+ }
+ this.featurePanel.add(men);
+ men.show(this.featurePanel, x, y);
+ }
+
+ public void setTableData()
+ {
+ alignmentHasFeatures = fr.buildGroupHash();
+ if (alignmentHasFeatures)
+ {
+ rebuildGroups();
+
+ }
+ resetTable(false);
+ }
+
+ /**
+ * rebuilds the group panel
+ */
+ public void rebuildGroups()
+ {
+ boolean rdrw = false;
+ if (groupPanel == null)
+ {
+ groupPanel = new Panel();
+ }
+ else
+ {
+ rdrw = true;
+ groupPanel.removeAll();
+ }
+
+ Enumeration gps = fr.featureGroups.keys();
+ while (gps.hasMoreElements())
+ {
+ String group = (String) gps.nextElement();
+ Boolean vis = (Boolean) fr.featureGroups.get(group);
+ Checkbox check = new MyCheckbox(group, vis.booleanValue(),
+ (fr.featureLinks != null && fr.featureLinks
+ .containsKey(group)));
+ check.addMouseListener(this);
+ check.setFont(new Font("Serif", Font.BOLD, 12));
+ check.addItemListener(this);
+ groupPanel.add(check);
+ }
+ if (rdrw)
+ {
+ groupPanel.validate();
+ }
+ }
+
+ // This routine adds and removes checkboxes depending on
+ // Group selection states
+ void resetTable(boolean groupsChanged)
+ {
+ SequenceFeature[] tmpfeatures;
+ String group = null, type;
+ Vector visibleChecks = new Vector();
+
+ for (int i = 0; i < av.alignment.getHeight(); i++)
+ {
+ if (av.alignment.getSequenceAt(i).getSequenceFeatures() == null)
+ {
+ continue;
+ }
+
+ tmpfeatures = av.alignment.getSequenceAt(i).getSequenceFeatures();
+ int index = 0;
+ while (index < tmpfeatures.length)
+ {
+ group = tmpfeatures[index].featureGroup;
+
+ if (group == null || fr.featureGroups.get(group) == null
+ || ((Boolean) fr.featureGroups.get(group)).booleanValue())
+ {
+ type = tmpfeatures[index].getType();
+ if (!visibleChecks.contains(type))
+ {
+ visibleChecks.addElement(type);
+ }
+ }
+ index++;
+ }
+ }
+
+ Component[] comps;
+ int cSize = featurePanel.getComponentCount();
+ MyCheckbox check;
+ // This will remove any checkboxes which shouldn't be
+ // visible
+ for (int i = 0; i < cSize; i++)
+ {
+ comps = featurePanel.getComponents();
+ check = (MyCheckbox) comps[i];
+ if (!visibleChecks.contains(check.type))
+ {
+ featurePanel.remove(i);
+ cSize--;
+ i--;
+ }
+ }
+
+ if (fr.renderOrder != null)
+ {
+ // First add the checks in the previous render order,
+ // in case the window has been closed and reopened
+ for (int ro = fr.renderOrder.length - 1; ro > -1; ro--)
+ {
+ String item = fr.renderOrder[ro];
+
+ if (!visibleChecks.contains(item))
+ {
+ continue;
+ }
+
+ visibleChecks.removeElement(item);
+
+ addCheck(false, item);
+ }
+ }
+
+ // now add checkboxes which should be visible,
+ // if they have not already been added
+ Enumeration en = visibleChecks.elements();
+
+ while (en.hasMoreElements())
+ {
+ addCheck(groupsChanged, en.nextElement().toString());
+ }
+
+ featurePanel.setLayout(new GridLayout(featurePanel.getComponentCount(),
+ 1, 10, 5));
+ featurePanel.validate();
+
+ if (scrollPane != null)
+ {
+ scrollPane.validate();
+ }
+
+ itemStateChanged(null);
+ }
+
+ /**
+ * 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
+ * @param type
+ * feature type to be checked for in the list.
+ */
+ void addCheck(boolean groupsChanged, String type)
+ {
+ boolean addCheck;
+ Component[] comps = featurePanel.getComponents();
+ MyCheckbox check;
+ addCheck = true;
+ for (int i = 0; i < featurePanel.getComponentCount(); i++)
+ {
+ check = (MyCheckbox) comps[i];
+ if (check.type.equals(type))
+ {
+ addCheck = false;
+ break;
+ }
+ }
+
+ if (addCheck)
+ {
+ boolean selected = false;
+ if (groupsChanged || av.featuresDisplayed.containsKey(type))
+ {
+ selected = true;
+ }
+
+ check = new MyCheckbox(
+ type,
+ selected,
+ (fr.featureLinks != null && fr.featureLinks.containsKey(type)),
+ fr.getFeatureStyle(type));
+
+ check.addMouseListener(this);
+ check.addMouseMotionListener(this);
+ check.addItemListener(this);
+ if (groupsChanged)
+ {
+ // add at beginning of stack.
+ featurePanel.add(check, 0);
+ }
+ else
+ {
+ // add at end of stack.
+ featurePanel.add(check);
+ }
+ }
+ }
+
+ public void actionPerformed(ActionEvent evt)
+ {
+ for (int i = 0; i < featurePanel.getComponentCount(); i++)
+ {
+ Checkbox check = (Checkbox) featurePanel.getComponent(i);
+ check.setState(!check.getState());
+ }
+ selectionChanged();
+ }
+
+ public void itemStateChanged(ItemEvent evt)
+ {
+ if (evt != null)
+ {
+ // Is the source a top level featureGroup?
+ Checkbox source = (Checkbox) evt.getSource();
+ if (fr.featureGroups.containsKey(source.getLabel()))
+ {
+ fr.featureGroups.put(source.getLabel(),
+ new Boolean(source.getState()));
+ ap.seqPanel.seqCanvas.repaint();
+ if (ap.overviewPanel != null)
+ {
+ ap.overviewPanel.updateOverviewImage();
+ }
+
+ resetTable(true);
+ return;
+ }
+ }
+ selectionChanged();
+ }
+
+ void selectionChanged()
+ {
+ Component[] comps = featurePanel.getComponents();
+ int cSize = comps.length;
+
+ Object[][] tmp = new Object[cSize][3];
+ int tmpSize = 0;
+ for (int i = 0; i < cSize; i++)
+ {
+ 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++;
+ }
+
+ Object[][] data = new Object[tmpSize][3];
+ System.arraycopy(tmp, 0, data, 0, tmpSize);
+
+ fr.setFeaturePriority(data);
+
+ ap.paintAlignment(true);
+ }
+
+ MyCheckbox selectedCheck;
+
+ boolean dragging = false;
+
+ public void mousePressed(MouseEvent evt)
+ {
+
+ selectedCheck = (MyCheckbox) evt.getSource();
+
+ if (fr.featureLinks != null
+ && fr.featureLinks.containsKey(selectedCheck.type))
+ {
+ if (evt.getX() > selectedCheck.stringWidth + 20)
+ {
+ evt.consume();
+ }
+ }
+
+ }
+
+ public void mouseDragged(MouseEvent evt)
+ {
+ if (((Component) evt.getSource()).getParent() != featurePanel)
+ {
+ return;
+ }
+ dragging = true;
+ }
+
+ public void mouseReleased(MouseEvent evt)
+ {
+ if (((Component) evt.getSource()).getParent() != featurePanel)
+ {
+ return;
+ }
+
+ Component comp = null;
+ Checkbox target = null;
+
+ int height = evt.getY() + evt.getComponent().getLocation().y;
+
+ if (height > featurePanel.getSize().height)
+ {
+
+ comp = featurePanel
+ .getComponent(featurePanel.getComponentCount() - 1);
+ }
+ else if (height < 0)
+ {
+ comp = featurePanel.getComponent(0);
+ }
+ else
+ {
+ comp = featurePanel.getComponentAt(evt.getX(), evt.getY()
+ + evt.getComponent().getLocation().y);
+ }
+
+ if (comp != null && comp instanceof Checkbox)
+ {
+ target = (Checkbox) comp;
+ }
+
+ if (selectedCheck != null && target != null && selectedCheck != target)
+ {
+ int targetIndex = -1;
+ for (int i = 0; i < featurePanel.getComponentCount(); i++)
+ {
+ if (target == featurePanel.getComponent(i))
+ {
+ targetIndex = i;
+ break;
+ }
+ }
+
+ featurePanel.remove(selectedCheck);
+ featurePanel.add(selectedCheck, targetIndex);
+ featurePanel.validate();
+ itemStateChanged(null);
+ }
+ }
+
+ 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()
+ {
+ featurePanel.removeAll();
+ resetTable(false);
+ ap.paintAlignment(true);
+ }
+
+ public void mouseEntered(MouseEvent evt)
+ {
+ }
+
+ public void mouseExited(MouseEvent evt)
+ {
+ }
+
+ public void mouseClicked(MouseEvent evt)
+ {
+ MyCheckbox check = (MyCheckbox) evt.getSource();
+ if ((evt.getModifiers() & InputEvent.BUTTON3_MASK) != 0)
+ {
+ this.popupSort(check, fr.minmax, evt.getX(), evt.getY());
+ }
+ 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("|")));
+ }
+ }
+
+ if (check.getParent() != featurePanel)
+ {
+ return;
+ }
+
+ if (evt.getClickCount() > 1)
+ {
+ 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));
+ }
+ }
+ }
+
+ public void mouseMoved(MouseEvent evt)
+ {
+ }
+
+ public void adjustmentValueChanged(AdjustmentEvent evt)
+ {
+ fr.transparency = ((float) (100 - transparency.getValue()) / 100f);
+ ap.seqPanel.seqCanvas.repaint();
+
+ }
+
+ 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,
+ (getSize().height - linkImage.getHeight(this)) / 2, this);
+ }
+ }
+ }
+
+ protected void sortByDens(String[] typ)
+ {
+ sortBy(typ, "Sort by Density", AlignmentSorter.FEATURE_DENSITY);
+ }
+
+ private String[] getDisplayedFeatureTypes()
+ {
+ String[] typ = null;
+ if (fr != null)
+ {
+ synchronized (fr.renderOrder)
+ {
+ typ = new String[fr.renderOrder.length];
+ System.arraycopy(fr.renderOrder, 0, typ, 0, typ.length);
+ for (int i = 0; i < typ.length; i++)
+ {
+ if (av.featuresDisplayed.get(typ[i]) == null)
+ {
+ typ[i] = null;
+ }
+ }
+ }
+ }
+ return typ;
+ }
+
+ protected void sortBy(String[] typ, String methodText, final String method)
+ {
+ if (typ == null)
+ {
+ typ = getDisplayedFeatureTypes();
+ }
+ String gps[] = null;
+ gps = fr.getGroups(true);
+ if (typ != null)
+ {
+ for (int i = 0; i < typ.length; i++)
+ {
+ System.err.println("Sorting on Types:" + typ[i]);
+ }
+ }
+ if (gps != null)
+ {
+
+ for (int i = 0; i < gps.length; i++)
+ {
+ System.err.println("Sorting on groups:" + gps[i]);
+ }
+ }
+ AlignmentPanel alignPanel = ap;
+ AlignmentI al = alignPanel.av.getAlignment();
+
+ int start, stop;
+ SequenceGroup sg = alignPanel.av.getSelectionGroup();
+ if (sg != null)
+ {
+ start = sg.getStartRes();
+ stop = sg.getEndRes();
+ }
+ else
+ {
+ start = 0;
+ stop = al.getWidth();
+ }
+ SequenceI[] oldOrder = al.getSequencesArray();
+ AlignmentSorter.sortByFeature(typ, gps, start, stop, al, method);
+ this.ap.alignFrame.addHistoryItem(new OrderCommand(methodText,
+ oldOrder, alignPanel.av.getAlignment()));
+ alignPanel.paintAlignment(true);
+
+ }
+
+ protected void sortByScore(String[] typ)
+ {
+ sortBy(typ, "Sort by Feature Score", AlignmentSorter.FEATURE_SCORE);
+ }
+
+}
git://source.jalview.org / jalview.git / blobdiff