-/*\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
-\r
-package jalview.appletgui;\r
-\r
-import jalview.datamodel.*;\r
-import java.awt.*;\r
-import java.util.*;\r
-\r
-public class FeatureRenderer\r
-{\r
- AlignViewport av;\r
-\r
- SequenceGroup currentSequenceGroup = null;\r
- SequenceGroup [] allGroups = null;\r
- Color resBoxColour;\r
- Graphics graphics;\r
-\r
- public FeatureRenderer(AlignViewport av)\r
- {\r
- this.av = av;\r
- }\r
-\r
-\r
- public void drawSequence(Graphics g,SequenceI seq,SequenceGroup [] sg, int start, int end, int x1, int y1, int width, int height)\r
- {\r
- Vector features = seq.getSequenceFeatures();\r
- Enumeration e = features.elements();\r
- while( e.hasMoreElements() )\r
- {\r
- SequenceFeature sf = (SequenceFeature)e.nextElement();\r
- if(sf.getStart()>seq.getEnd())\r
- continue;\r
-\r
- int fstart = seq.findIndex(sf.getStart())-1;\r
- int fend = seq.findIndex(sf.getEnd())-1;\r
-\r
- if( (fstart<=end && fend>=start) )\r
- {\r
- if(fstart<0) // fix for if the feature we have starts before the sequence start,\r
- fstart = 0;// but the feature end is still valid!!\r
-\r
- if(fstart==fend)\r
- {\r
- g.setColor(Color.red);\r
- g.fillRoundRect( (fstart - start) * width, y1, width, height, 4,4);\r
- g.setColor(Color.white);\r
-\r
- char s = seq.getSequence().charAt(fstart);\r
- FontMetrics fm = g.getFontMetrics();\r
- int charOffset = (width - fm.charWidth(s))/2;\r
- int pady = height/5;\r
- g.drawString(String.valueOf(s), charOffset + x1 + width * (fstart - start), y1 + height - pady);\r
-\r
- }\r
- else\r
- {\r
- for (int i = fstart; i <= fend; i++)\r
- {\r
- char s = seq.getSequence().charAt(i);\r
- if( jalview.util.Comparison.isGap(s) )\r
- continue;\r
-\r
- g.setColor(Color.blue);\r
- g.fillRect( (i-start) * width, y1, width, height);\r
-\r
- g.setColor(Color.white);\r
-\r
- FontMetrics fm = g.getFontMetrics();\r
- int charOffset = (width - fm.charWidth(s)) / 2;\r
- int pady = height / 5;\r
- g.drawString(String.valueOf(s),\r
- charOffset + x1 + width * (i-start),\r
- y1 + height - pady);\r
- }\r
- }\r
- }\r
-\r
- }\r
- }\r
-\r
-}\r
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ 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 <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
+package jalview.appletgui;
+
+import jalview.api.FeatureColourI;
+import jalview.datamodel.SearchResults;
+import jalview.datamodel.SequenceFeature;
+import jalview.datamodel.SequenceI;
+import jalview.io.FeaturesFile;
+import jalview.schemes.Colour;
+import jalview.schemes.FeatureColour;
+import jalview.schemes.UserColourScheme;
+import jalview.util.ColorUtils;
+import jalview.util.MessageManager;
+import jalview.viewmodel.AlignmentViewport;
+
+import java.awt.BorderLayout;
+import java.awt.Button;
+import java.awt.Choice;
+import java.awt.Color;
+import java.awt.Dimension;
+import java.awt.Font;
+import java.awt.Graphics;
+import java.awt.GridLayout;
+import java.awt.Label;
+import java.awt.Panel;
+import java.awt.ScrollPane;
+import java.awt.TextArea;
+import java.awt.TextField;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+import java.awt.event.MouseAdapter;
+import java.awt.event.MouseEvent;
+import java.util.Hashtable;
+
+/**
+ * DOCUMENT ME!
+ *
+ * @author $author$
+ * @version $Revision$
+ */
+public class FeatureRenderer extends
+ jalview.renderer.seqfeatures.FeatureRenderer
+{
+ // Holds web links for feature groups and feature types
+ // in the form label|link
+ Hashtable featureLinks = null;
+
+ static String lastFeatureAdded;
+
+ static String lastFeatureGroupAdded;
+
+ static String lastDescriptionAdded;
+
+ int featureIndex = 0;
+
+ boolean deleteFeature = false;
+
+ FeatureColourPanel colourPanel;
+
+ /**
+ * Creates a new FeatureRenderer object.
+ *
+ * @param av
+ */
+ public FeatureRenderer(AlignmentViewport av)
+ {
+ super(av);
+ }
+
+ class FeatureColourPanel extends Panel
+ {
+ String label = "";
+
+ private Color maxCol;
+
+ private boolean isColourByLabel, isGcol;
+
+ /**
+ * render a feature style in the amend feature dialog box
+ */
+ public void updateColor(FeatureColourI newcol)
+ {
+ Color bg = null;
+ String vlabel = "";
+ if (newcol.isSimpleColour())
+ {
+ bg = ColorUtils.getColor(newcol.getColour());
+ setBackground(bg);
+ }
+ else
+ {
+ if (newcol.isAboveThreshold())
+ {
+ vlabel += " (>)";
+ }
+ else if (newcol.isBelowThreshold())
+ {
+ vlabel += " (<)";
+ }
+
+ if (isColourByLabel = newcol.isColourByLabel())
+ {
+ setBackground(bg = Color.white);
+ vlabel += " (by Label)";
+ }
+ else
+ {
+ setBackground(bg = ColorUtils.getColor(newcol.getMinColour()));
+ maxCol = ColorUtils.getColor(newcol.getMaxColour());
+ }
+ }
+ label = vlabel;
+ setBackground(bg);
+ repaint();
+ }
+
+ FeatureColourPanel()
+ {
+ super(null);
+ }
+
+ @Override
+ public void paint(Graphics g)
+ {
+ Dimension d = getSize();
+ if (isGcol)
+ {
+ if (isColourByLabel)
+ {
+ g.setColor(Color.white);
+ g.fillRect(d.width / 2, 0, d.width / 2, d.height);
+ g.setColor(Color.black);
+ Font f = new Font("Verdana", Font.PLAIN, 10);
+ g.setFont(f);
+ g.drawString(MessageManager.getString("label.label"), 0, 0);
+ }
+ else
+ {
+ g.setColor(maxCol);
+ g.fillRect(d.width / 2, 0, d.width / 2, d.height);
+
+ }
+ }
+ }
+
+ }
+
+ boolean amendFeatures(final SequenceI[] sequences,
+ final SequenceFeature[] features, boolean newFeatures,
+ final AlignmentPanel ap)
+ {
+ Panel bigPanel = new Panel(new BorderLayout());
+ final TextField name = new TextField(16);
+ final TextField source = new TextField(16);
+ final TextArea description = new TextArea(3, 35);
+ final TextField start = new TextField(8);
+ final TextField end = new TextField(8);
+ final Choice overlaps;
+ Button deleteButton = new Button("Delete");
+ deleteFeature = false;
+
+ colourPanel = new FeatureColourPanel();
+ colourPanel.setSize(110, 15);
+ final FeatureRenderer fr = this;
+
+ Panel panel = new Panel(new GridLayout(3, 1));
+
+ featureIndex = 0; // feature to be amended.
+ Panel tmp;
+
+ // /////////////////////////////////////
+ // /MULTIPLE FEATURES AT SELECTED RESIDUE
+ if (!newFeatures && features.length > 1)
+ {
+ panel = new Panel(new GridLayout(4, 1));
+ tmp = new Panel();
+ tmp.add(new Label("Select Feature: "));
+ overlaps = new Choice();
+ for (int i = 0; i < features.length; i++)
+ {
+ String item = features[i].getType() + "/" + features[i].getBegin()
+ + "-" + features[i].getEnd();
+
+ if (features[i].getFeatureGroup() != null)
+ {
+ item += " (" + features[i].getFeatureGroup() + ")";
+ }
+
+ overlaps.addItem(item);
+ }
+
+ tmp.add(overlaps);
+
+ overlaps.addItemListener(new java.awt.event.ItemListener()
+ {
+ @Override
+ public void itemStateChanged(java.awt.event.ItemEvent e)
+ {
+ int index = overlaps.getSelectedIndex();
+ if (index != -1)
+ {
+ featureIndex = index;
+ name.setText(features[index].getType());
+ description.setText(features[index].getDescription());
+ source.setText(features[index].getFeatureGroup());
+ start.setText(features[index].getBegin() + "");
+ end.setText(features[index].getEnd() + "");
+
+ SearchResults highlight = new SearchResults();
+ highlight.addResult(sequences[0], features[index].getBegin(),
+ features[index].getEnd());
+
+ ap.seqPanel.seqCanvas.highlightSearchResults(highlight);
+
+ }
+ FeatureColourI col = getFeatureStyle(name.getText());
+ if (col == null)
+ {
+ Color generatedColour = UserColourScheme
+ .createColourFromName(name.getText());
+ col = new FeatureColour(new Colour(generatedColour));
+ }
+
+ colourPanel.updateColor(col);
+ }
+ });
+
+ panel.add(tmp);
+ }
+ // ////////
+ // ////////////////////////////////////
+
+ tmp = new Panel();
+ panel.add(tmp);
+ tmp.add(new Label(MessageManager.getString("label.name:"), Label.RIGHT));
+ tmp.add(name);
+
+ tmp = new Panel();
+ panel.add(tmp);
+ tmp.add(new Label(MessageManager.getString("label.group:"), Label.RIGHT));
+ tmp.add(source);
+
+ tmp = new Panel();
+ panel.add(tmp);
+ tmp.add(new Label(MessageManager.getString("label.colour"), Label.RIGHT));
+ tmp.add(colourPanel);
+
+ bigPanel.add(panel, BorderLayout.NORTH);
+
+ panel = new Panel();
+ panel.add(new Label(MessageManager.getString("label.description:"),
+ Label.RIGHT));
+ panel.add(new ScrollPane().add(description));
+
+ if (!newFeatures)
+ {
+ bigPanel.add(panel, BorderLayout.SOUTH);
+
+ panel = new Panel();
+ panel.add(new Label(MessageManager.getString("label.start"),
+ Label.RIGHT));
+ panel.add(start);
+ panel.add(new Label(MessageManager.getString("label.end"),
+ Label.RIGHT));
+ panel.add(end);
+ bigPanel.add(panel, BorderLayout.CENTER);
+ }
+ else
+ {
+ bigPanel.add(panel, BorderLayout.CENTER);
+ }
+
+ if (lastFeatureAdded == null)
+ {
+ if (features[0].type != null)
+ {
+ lastFeatureAdded = features[0].type;
+ }
+ else
+ {
+ lastFeatureAdded = "feature_1";
+ }
+ }
+
+ if (lastFeatureGroupAdded == null)
+ {
+ if (features[0].featureGroup != null)
+ {
+ lastFeatureGroupAdded = features[0].featureGroup;
+ }
+ else
+ {
+ lastFeatureAdded = "Jalview";
+ }
+ }
+
+ String title = newFeatures ? MessageManager
+ .getString("label.create_new_sequence_features")
+ : MessageManager.formatMessage("label.amend_delete_features",
+ new String[] { sequences[0].getName() });
+
+ final JVDialog dialog = new JVDialog(ap.alignFrame, title, true, 385,
+ 240);
+
+ dialog.setMainPanel(bigPanel);
+
+ if (newFeatures)
+ {
+ name.setText(lastFeatureAdded);
+ source.setText(lastFeatureGroupAdded);
+ }
+ else
+ {
+ dialog.ok.setLabel(MessageManager.getString("label.amend"));
+ dialog.buttonPanel.add(deleteButton, 1);
+ deleteButton.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent evt)
+ {
+ deleteFeature = true;
+ dialog.setVisible(false);
+ }
+ });
+ name.setText(features[0].getType());
+ source.setText(features[0].getFeatureGroup());
+ }
+
+ start.setText(features[0].getBegin() + "");
+ end.setText(features[0].getEnd() + "");
+ description.setText(features[0].getDescription());
+ // lookup (or generate) the feature colour
+ FeatureColourI fcol = getFeatureStyle(name.getText());
+ // simply display the feature color in a box
+ colourPanel.updateColor(fcol);
+ dialog.setResizable(true);
+ // TODO: render the graduated color in the box.
+ colourPanel.addMouseListener(new MouseAdapter()
+ {
+ @Override
+ public void mousePressed(MouseEvent evt)
+ {
+ if (!colourPanel.isGcol)
+ {
+ new UserDefinedColours(fr, ap.alignFrame);
+ }
+ else
+ {
+ new FeatureColourChooser(ap.alignFrame, name.getText());
+ dialog.transferFocus();
+ }
+ }
+ });
+ dialog.setVisible(true);
+
+ FeaturesFile ffile = new FeaturesFile();
+
+ if (dialog.accept)
+ {
+ // This ensures that the last sequence
+ // is refreshed and new features are rendered
+ lastSeq = null;
+ lastFeatureAdded = name.getText().trim();
+ lastFeatureGroupAdded = source.getText().trim();
+ lastDescriptionAdded = description.getText().replace('\n', ' ');
+ }
+
+ if (lastFeatureGroupAdded != null && lastFeatureGroupAdded.length() < 1)
+ {
+ lastFeatureGroupAdded = null;
+ }
+
+ if (!newFeatures)
+ {
+
+ SequenceFeature sf = features[featureIndex];
+ if (dialog.accept)
+ {
+ sf.type = lastFeatureAdded;
+ sf.featureGroup = lastFeatureGroupAdded;
+ sf.description = lastDescriptionAdded;
+ if (!colourPanel.isGcol)
+ {
+ // update colour - otherwise its already done.
+ setColour(
+ sf.type,
+ new FeatureColour(new Colour(colourPanel.getBackground())));
+ }
+ try
+ {
+ sf.begin = Integer.parseInt(start.getText());
+ sf.end = Integer.parseInt(end.getText());
+ } catch (NumberFormatException ex)
+ {
+ }
+
+ ffile.parseDescriptionHTML(sf, false);
+ setVisible(lastFeatureAdded); // if user edited name then make sure new
+ // type is visible
+ }
+ if (deleteFeature)
+ {
+ sequences[0].deleteFeature(sf);
+ }
+
+ }
+ else
+ {
+ if (dialog.accept && name.getText().length() > 0)
+ {
+ for (int i = 0; i < sequences.length; i++)
+ {
+ features[i].type = lastFeatureAdded;
+ features[i].featureGroup = lastFeatureGroupAdded;
+ features[i].description = lastDescriptionAdded;
+ sequences[i].addSequenceFeature(features[i]);
+ ffile.parseDescriptionHTML(features[i], false);
+ }
+
+ Color newColour = colourPanel.getBackground();
+ // setColour(lastFeatureAdded, fcol);
+
+ if (lastFeatureGroupAdded != null)
+ {
+ setGroupVisibility(lastFeatureGroupAdded, true);
+ }
+ setColour(lastFeatureAdded,
+ new FeatureColour(new Colour(newColour))); // was fcol
+ setVisible(lastFeatureAdded);
+ findAllFeatures(false); // different to original applet behaviour ?
+ // findAllFeatures();
+ }
+ else
+ {
+ // no update to the alignment
+ return false;
+ }
+ }
+ // refresh the alignment and the feature settings dialog
+ if (((jalview.appletgui.AlignViewport) av).featureSettings != null)
+ {
+ ((jalview.appletgui.AlignViewport) av).featureSettings.refreshTable();
+ }
+ // findAllFeatures();
+
+ ap.paintAlignment(true);
+
+ return true;
+ }
+}
git://source.jalview.org / jalview.git / blobdiff