X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FFeatureRenderer.java;h=3c2715f28bb715abdaed3176ade207245f1eb59b;hb=fb548a8458941602b0b8b45da5aaf60206e10ec2;hp=a8412f0d1137f541de1c67dee9dbfc5fe08bdf4f;hpb=ec955aa655d8320258b91eb079bc57f688cd0a07;p=jalview.git
diff --git a/src/jalview/appletgui/FeatureRenderer.java b/src/jalview/appletgui/FeatureRenderer.java
old mode 100755
new mode 100644
index a8412f0..3c2715f
--- a/src/jalview/appletgui/FeatureRenderer.java
+++ b/src/jalview/appletgui/FeatureRenderer.java
@@ -1,79 +1,525 @@
-package jalview.appletgui;
-
-import jalview.datamodel.*;
-import java.awt.*;
-import java.util.*;
-
-public class FeatureRenderer
-{
- AlignViewport av;
-
- SequenceGroup currentSequenceGroup = null;
- SequenceGroup [] allGroups = null;
- Color resBoxColour;
- Graphics graphics;
-
- public FeatureRenderer(AlignViewport av)
- {
- this.av = av;
- }
-
-
- public void drawSequence(Graphics g,SequenceI seq,SequenceGroup [] sg, int start, int end, int x1, int y1, int width, int height)
- {
- Vector features = seq.getSequenceFeatures();
- Enumeration e = features.elements();
- while( e.hasMoreElements() )
- {
- SequenceFeature sf = (SequenceFeature)e.nextElement();
- if(sf.getStart()>seq.getEnd())
- continue;
-
- int fstart = seq.findIndex(sf.getStart())-1;
- int fend = seq.findIndex(sf.getEnd())-1;
-
- if( (fstart<=end && fend>=start) )
- {
- if(fstart<0) // fix for if the feature we have starts before the sequence start,
- fstart = 0;// but the feature end is still valid!!
-
- if(fstart==fend)
- {
- g.setColor(Color.red);
- g.fillRoundRect( (fstart - start) * width, y1, width, height, 4,4);
- g.setColor(Color.white);
-
- char s = seq.getSequence().charAt(fstart);
- FontMetrics fm = g.getFontMetrics();
- int charOffset = (width - fm.charWidth(s))/2;
- int pady = height/5;
- g.drawString(String.valueOf(s), charOffset + x1 + width * (fstart - start), y1 + height - pady);
-
- }
- else
- {
- for (int i = fstart; i <= fend; i++)
- {
- char s = seq.getSequence().charAt(i);
- if( jalview.util.Comparison.isGap(s) )
- continue;
-
- g.setColor(Color.blue);
- g.fillRect( (i-start) * width, y1, width, height);
-
- g.setColor(Color.white);
-
- FontMetrics fm = g.getFontMetrics();
- int charOffset = (width - fm.charWidth(s)) / 2;
- int pady = height / 5;
- g.drawString(String.valueOf(s),
- charOffset + x1 + width * (i-start),
- y1 + height - pady);
- }
- }
- }
-
- }
- }
-
-}
+/*
+ * 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 .
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
+package jalview.appletgui;
+
+import jalview.api.FeatureColourI;
+import jalview.datamodel.SearchResults;
+import jalview.datamodel.SearchResultsI;
+import jalview.datamodel.SequenceFeature;
+import jalview.datamodel.SequenceI;
+import jalview.io.FeaturesFile;
+import jalview.schemes.FeatureColour;
+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.FlowLayout;
+import java.awt.Font;
+import java.awt.Frame;
+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.awt.event.TextEvent;
+import java.awt.event.TextListener;
+import java.util.Hashtable;
+import java.util.List;
+
+/**
+ * DOCUMENT ME!
+ *
+ * @author $author$
+ * @version $Revision$
+ */
+public class FeatureRenderer extends
+ jalview.renderer.seqfeatures.FeatureRenderer
+{
+ /*
+ * creating a new feature defaults to the type and group as
+ * the last one created
+ */
+ static String lastFeatureAdded = "feature_1";
+
+ static String lastFeatureGroupAdded = "Jalview";
+
+ // Holds web links for feature groups and feature types
+ // in the form label|link
+ Hashtable featureLinks = null;
+
+ /**
+ * Creates a new FeatureRenderer object.
+ *
+ * @param av
+ */
+ public FeatureRenderer(AlignmentViewport av)
+ {
+ super(av);
+
+ }
+
+ int featureIndex = 0;
+
+ boolean deleteFeature = false;
+
+ FeatureColourPanel colourPanel;
+
+ 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 = 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 = newcol.getMinColour());
+ maxCol = 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);
+
+ }
+ }
+ }
+
+ }
+
+ /**
+ * Shows a dialog allowing the user to create, or amend or delete, sequence
+ * features. If null in the supplied feature(s), feature type and group
+ * default to those for the last feature created (with initial defaults of
+ * "feature_1" and "Jalview").
+ *
+ * @param sequences
+ * @param features
+ * @param create
+ * @param ap
+ * @return
+ */
+ boolean amendFeatures(final List sequences,
+ final List features, boolean create,
+ final AlignmentPanel ap)
+ {
+ final Panel bigPanel = new Panel(new BorderLayout());
+ final TextField name = new TextField(16);
+ final TextField group = 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;
+
+ name.addTextListener(new TextListener()
+ {
+ @Override
+ public void textValueChanged(TextEvent e)
+ {
+ warnIfTypeHidden(ap.alignFrame, name.getText());
+ }
+ });
+ group.addTextListener(new TextListener()
+ {
+ @Override
+ public void textValueChanged(TextEvent e)
+ {
+ warnIfGroupHidden(ap.alignFrame, group.getText());
+ }
+ });
+ 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 (!create && features.size() > 1)
+ {
+ panel = new Panel(new GridLayout(4, 1));
+ tmp = new Panel();
+ tmp.add(new Label("Select Feature: "));
+ overlaps = new Choice();
+ for (SequenceFeature sf : features)
+ {
+ String item = sf.getType() + "/" + sf.getBegin() + "-"
+ + sf.getEnd();
+ if (sf.getFeatureGroup() != null)
+ {
+ item += " (" + sf.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;
+ SequenceFeature sf = features.get(index);
+ name.setText(sf.getType());
+ description.setText(sf.getDescription());
+ group.setText(sf.getFeatureGroup());
+ start.setText(sf.getBegin() + "");
+ end.setText(sf.getEnd() + "");
+
+ SearchResultsI highlight = new SearchResults();
+ highlight.addResult(sequences.get(0), sf.getBegin(),
+ sf.getEnd());
+
+ ap.seqPanel.seqCanvas.highlightSearchResults(highlight);
+
+ }
+ FeatureColourI col = getFeatureStyle(name.getText());
+ if (col == null)
+ {
+ Color generatedColour = ColorUtils.createColourFromName(name
+ .getText());
+ col = new FeatureColour(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(group);
+
+ 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 (!create)
+ {
+ 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);
+ }
+
+ /*
+ * use defaults for type and group (and update them on Confirm) only
+ * if feature type has not been supplied by the caller
+ * (e.g. for Amend, or create features from Find)
+ */
+ SequenceFeature firstFeature = features.get(0);
+ boolean useLastDefaults = firstFeature.getType() == null;
+ String featureType = useLastDefaults ? lastFeatureAdded : firstFeature
+ .getType();
+ String featureGroup = useLastDefaults ? lastFeatureGroupAdded
+ : firstFeature.getFeatureGroup();
+
+ String title = create ? MessageManager
+ .getString("label.create_new_sequence_features")
+ : MessageManager.formatMessage("label.amend_delete_features",
+ new String[] { sequences.get(0).getName() });
+
+ final JVDialog dialog = new JVDialog(ap.alignFrame, title, true, 385,
+ 240);
+
+ dialog.setMainPanel(bigPanel);
+
+ name.setText(featureType);
+ group.setText(featureGroup);
+
+ if (!create)
+ {
+ 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);
+ }
+ });
+ }
+
+ start.setText(firstFeature.getBegin() + "");
+ end.setText(firstFeature.getEnd() + "");
+ description.setText(firstFeature.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();
+
+ /*
+ * only update default type and group if we used defaults
+ */
+ String enteredType = name.getText().trim();
+ if (dialog.accept && useLastDefaults)
+ {
+ lastFeatureAdded = enteredType;
+ lastFeatureGroupAdded = group.getText().trim();
+ }
+
+ if (!create)
+ {
+ SequenceFeature sf = features.get(featureIndex);
+ if (dialog.accept)
+ {
+ sf.type = enteredType;
+ sf.featureGroup = group.getText().trim();
+ if (sf.featureGroup != null && sf.featureGroup.length() < 1)
+ {
+ sf.featureGroup = null;
+ }
+ sf.description = description.getText().replace('\n', ' ');
+ if (!colourPanel.isGcol)
+ {
+ // update colour - otherwise its already done.
+ setColour(sf.type, new FeatureColour(colourPanel.getBackground()));
+ }
+ try
+ {
+ sf.begin = Integer.parseInt(start.getText());
+ sf.end = Integer.parseInt(end.getText());
+ } catch (NumberFormatException ex)
+ {
+ //
+ }
+ boolean typeOrGroupChanged = (!featureType.equals(sf.type) || !featureGroup
+ .equals(sf.featureGroup));
+
+ ffile.parseDescriptionHTML(sf, false);
+ if (typeOrGroupChanged)
+ {
+ featuresAdded();
+ }
+ }
+ if (deleteFeature)
+ {
+ sequences.get(0).deleteFeature(sf);
+ // ensure Feature Settings reflects removal of feature / group
+ featuresAdded();
+ }
+ }
+ else
+ {
+ /*
+ * adding feature(s)
+ */
+ if (dialog.accept && name.getText().length() > 0)
+ {
+ for (int i = 0; i < sequences.size(); i++)
+ {
+ features.get(i).type = enteredType;
+ features.get(i).featureGroup = group.getText().trim();
+ features.get(i).description = description.getText()
+ .replace('\n', ' ');
+ sequences.get(i).addSequenceFeature(features.get(i));
+ ffile.parseDescriptionHTML(features.get(i), false);
+ }
+
+ Color newColour = colourPanel.getBackground();
+ // setColour(lastFeatureAdded, fcol);
+
+ setColour(enteredType, new FeatureColour(newColour)); // was fcol
+ featuresAdded();
+ }
+ 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;
+ }
+
+ protected void warnIfGroupHidden(Frame frame, String group)
+ {
+ if (featureGroups.containsKey(group) && !featureGroups.get(group))
+ {
+ String msg = MessageManager.formatMessage("label.warning_hidden",
+ MessageManager.getString("label.group"), group);
+ showWarning(frame, msg);
+ }
+ }
+
+ protected void warnIfTypeHidden(Frame frame, String type)
+ {
+ if (getRenderOrder().contains(type))
+ {
+ if (!showFeatureOfType(type))
+ {
+ String msg = MessageManager.formatMessage("label.warning_hidden",
+ MessageManager.getString("label.feature_type"), type);
+ showWarning(frame, msg);
+ }
+ }
+ }
+
+ /**
+ * @param frame
+ * @param msg
+ */
+ protected void showWarning(Frame frame, String msg)
+ {
+ JVDialog d = new JVDialog(frame, "", true, 350, 200);
+ Panel mp = new Panel();
+ d.ok.setLabel(MessageManager.getString("action.ok"));
+ d.cancel.setVisible(false);
+ mp.setLayout(new FlowLayout());
+ mp.add(new Label(msg));
+ d.setMainPanel(mp);
+ d.setVisible(true);
+ }
+}