/*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, 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
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Copyright (C) 2015 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.
- *
- * 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 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 <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.appletgui;
-import java.util.*;
-
-import java.awt.*;
-
-import jalview.datamodel.*;
+import jalview.datamodel.SearchResults;
+import jalview.datamodel.SequenceFeature;
+import jalview.datamodel.SequenceI;
+import jalview.schemes.AnnotationColourGradient;
+import jalview.schemes.GraduatedColor;
+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.util.Hashtable;
/**
* DOCUMENT ME!
- *
+ *
* @author $author$
* @version $Revision$
*/
-public class FeatureRenderer
+public class FeatureRenderer extends
+ jalview.renderer.seqfeatures.FeatureRenderer
{
- AlignViewport av;
-
- Hashtable featureColours = new Hashtable();
-
- // A higher level for grouping features of a
- // particular type
- Hashtable featureGroups = null;
// Holds web links for feature groups and feature types
// in the form label|link
Hashtable featureLinks = null;
- // This is actually an Integer held in the hashtable,
- // Retrieved using the key feature type
- Object currentColour;
-
- String[] renderOrder;
-
- FontMetrics fm;
- int charOffset;
-
- float transparency = 1f;
-
- TransparencySetter transparencySetter = null;
-
/**
* Creates a new FeatureRenderer object.
- *
- * @param av DOCUMENT ME!
+ *
+ * @param av
+ * DOCUMENT ME!
*/
- public FeatureRenderer(AlignViewport av)
+ public FeatureRenderer(AlignmentViewport av)
{
+ super();
this.av = av;
- if (!System.getProperty("java.version").startsWith("1.1"))
- {
- transparencySetter = new TransparencySetter();
- }
- }
-
- public void transferSettings(FeatureRenderer fr)
- {
- renderOrder = fr.renderOrder;
- featureGroups = fr.featureGroups;
- featureColours = fr.featureColours;
- transparency = fr.transparency;
+ setTransparencyAvailable(!System.getProperty("java.version")
+ .startsWith("1.1"));
}
- public Color findFeatureColour(Color initialCol, SequenceI seq, int i)
- {
- overview = true;
- if (!av.showSequenceFeatures)
- {
- return initialCol;
- }
+ static String lastFeatureAdded;
- lastSequence = seq;
- sequenceFeatures = lastSequence.getSequenceFeatures();
- if (sequenceFeatures == null)
- {
- return initialCol;
- }
+ static String lastFeatureGroupAdded;
- sfSize = sequenceFeatures.length;
+ static String lastDescriptionAdded;
- if (jalview.util.Comparison.isGap(lastSequence.getCharAt(i)))
- {
- return Color.white;
- }
+ int featureIndex = 0;
- currentColour = null;
+ boolean deleteFeature = false;
- drawSequence(null, lastSequence, lastSequence.findPosition(i), -1, -1);
+ FeatureColourPanel colourPanel;
- if (currentColour == null)
- {
- return initialCol;
- }
+ class FeatureColourPanel extends Panel
+ {
+ String label = "";
- return new Color( ( (Integer) currentColour).intValue());
- }
+ private Color maxCol;
- /**
- * This is used by the Molecule Viewer to get the accurate colour
- * of the rendered sequence
- */
- boolean overview = false;
+ private boolean isColourByLabel, isGcol;
- int white = Color.white.getRGB();
- public int findFeatureColour(int initialCol, int seqIndex, int column)
- {
- if (!av.showSequenceFeatures)
+ /**
+ * render a feature style in the amend feature dialog box
+ */
+ public void updateColor(Object newcol)
{
- return initialCol;
- }
- if (seqIndex != lastSequenceIndex)
- {
- lastSequence = av.alignment.getSequenceAt(seqIndex);
- lastSequenceIndex = seqIndex;
- sequenceFeatures = lastSequence.getSequenceFeatures();
- if (sequenceFeatures == null)
+ Color bg, col = null;
+ GraduatedColor gcol = null;
+ String vlabel = "";
+ if (newcol instanceof Color)
{
- return initialCol;
+ isGcol = false;
+ col = (Color) newcol;
+ gcol = null;
}
-
- sfSize = sequenceFeatures.length;
+ else if (newcol instanceof GraduatedColor)
+ {
+ isGcol = true;
+ gcol = (GraduatedColor) newcol;
+ col = null;
+ }
+ else
+ {
+ throw new Error(
+ MessageManager
+ .getString("error.invalid_colour_for_mycheckbox"));
+ }
+ if (col != null)
+ {
+ setBackground(bg = col);
+ }
+ else
+ {
+ if (gcol.getThreshType() != AnnotationColourGradient.NO_THRESHOLD)
+ {
+ vlabel += " "
+ + ((gcol.getThreshType() == AnnotationColourGradient.ABOVE_THRESHOLD) ? "(>)"
+ : "(<)");
+ }
+ if (isColourByLabel = gcol.isColourByLabel())
+ {
+ setBackground(bg = Color.white);
+ vlabel += " (by Label)";
+ }
+ else
+ {
+ setBackground(bg = gcol.getMinColor());
+ maxCol = gcol.getMaxColor();
+ }
+ }
+ label = vlabel;
+ setBackground(bg);
+ repaint();
}
- if (jalview.util.Comparison.isGap(lastSequence.getCharAt(column)))
+ FeatureColourPanel()
{
- return Color.white.getRGB();
+ super(null);
}
- currentColour = null;
-
- drawSequence(null, lastSequence, lastSequence.findPosition(column), -1, -1);
-
- if (currentColour == null)
+ public void paint(Graphics g)
{
- return initialCol;
+ 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);
+
+ }
+ }
}
- return ( (Integer) currentColour).intValue();
}
- /**
- * DOCUMENT ME!
- *
- * @param g DOCUMENT ME!
- * @param seq DOCUMENT ME!
- * @param sg DOCUMENT ME!
- * @param start DOCUMENT ME!
- * @param end DOCUMENT ME!
- * @param x1 DOCUMENT ME!
- * @param y1 DOCUMENT ME!
- * @param width DOCUMENT ME!
- * @param height DOCUMENT ME!
- */
- // String type;
- // SequenceFeature sf;
- int lastSequenceIndex = -1;
- SequenceI lastSequence;
- SequenceFeature[] sequenceFeatures;
- int sfSize, sfindex, spos, epos;
-
- public void drawSequence(Graphics g, SequenceI seq,
- int start, int end, int y1)
+ boolean amendFeatures(final SequenceI[] sequences,
+ final SequenceFeature[] features, boolean newFeatures,
+ final AlignmentPanel ap)
{
- if (seq.getSequenceFeatures() == null
- || seq.getSequenceFeatures().length == 0)
+ 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)
{
- return;
- }
+ 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 (transparencySetter != null && g != null)
- {
- transparencySetter.setTransparency(g, transparency);
- }
-
- if (lastSequence == null || seq != lastSequence || sequenceFeatures!=seq.getSequenceFeatures())
- {
- lastSequence = seq;
- sequenceFeatures = seq.getSequenceFeatures();
- sfSize = sequenceFeatures.length;
- }
+ if (features[i].getFeatureGroup() != null)
+ {
+ item += " (" + features[i].getFeatureGroup() + ")";
+ }
- if (av.featuresDisplayed == null || renderOrder == null)
- {
- findAllFeatures();
- if (av.featuresDisplayed.size() < 1)
- {
- return;
+ overlaps.addItem(item);
}
- sequenceFeatures = seq.getSequenceFeatures();
- sfSize = sequenceFeatures.length;
- }
- if (!overview)
- {
- spos = lastSequence.findPosition(start);
- epos = lastSequence.findPosition(end);
- if (g != null)
- {
- fm = g.getFontMetrics();
- }
- }
- String type;
- for (int renderIndex = 0; renderIndex < renderOrder.length; renderIndex++)
- {
- type = renderOrder[renderIndex];
- if (!av.featuresDisplayed.containsKey(type))
- {
- continue;
- }
+ tmp.add(overlaps);
- // loop through all features in sequence to find
- // current feature to render
- for (sfindex = 0; sfindex < sfSize; sfindex++)
+ overlaps.addItemListener(new java.awt.event.ItemListener()
{
- if (!sequenceFeatures[sfindex].type.equals(type))
+ public void itemStateChanged(java.awt.event.ItemEvent e)
{
- continue;
- }
+ 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() + "");
- if (featureGroups != null
- && sequenceFeatures[sfindex].featureGroup != null
- &&
- featureGroups.containsKey(sequenceFeatures[sfindex].featureGroup)
- &&
- ! ( (Boolean) featureGroups.get(sequenceFeatures[sfindex].
- featureGroup)).
- booleanValue())
- {
- continue;
- }
+ SearchResults highlight = new SearchResults();
+ highlight.addResult(sequences[0], features[index].getBegin(),
+ features[index].getEnd());
- if (!overview && (sequenceFeatures[sfindex].getBegin() > epos
- || sequenceFeatures[sfindex].getEnd() < spos))
- {
- continue;
- }
+ ap.seqPanel.seqCanvas.highlightSearchResults(highlight);
- if (overview)
- {
- if (sequenceFeatures[sfindex].begin <= start &&
- sequenceFeatures[sfindex].end >= start)
+ }
+ Object col = getFeatureStyle(name.getText());
+ if (col == null)
{
- currentColour = av.featuresDisplayed.get(sequenceFeatures[sfindex].
- type);
+ col = new jalview.schemes.UserColourScheme()
+ .createColourFromName(name.getText());
}
+ colourPanel.updateColor(col);
}
- else if (sequenceFeatures[sfindex].type.equals("disulfide bond"))
- {
+ });
- renderFeature(g, seq,
- seq.findIndex(sequenceFeatures[sfindex].begin) - 1,
- seq.findIndex(sequenceFeatures[sfindex].begin) - 1,
- new Color( ( (Integer) av.featuresDisplayed.get(
- sequenceFeatures[sfindex].type)).intValue()),
- start, end, y1);
- renderFeature(g, seq,
- seq.findIndex(sequenceFeatures[sfindex].end) - 1,
- seq.findIndex(sequenceFeatures[sfindex].end) - 1,
- new Color( ( (Integer) av.featuresDisplayed.get(
- sequenceFeatures[sfindex].type)).intValue()),
- start, end, y1);
+ panel.add(tmp);
+ }
+ // ////////
+ // ////////////////////////////////////
- }
- else
- {
- renderFeature(g, seq,
- seq.findIndex(sequenceFeatures[sfindex].begin) - 1,
- seq.findIndex(sequenceFeatures[sfindex].end) - 1,
- getColour(sequenceFeatures[sfindex].type),
- start, end, y1);
- }
+ tmp = new Panel();
+ panel.add(tmp);
+ tmp.add(new Label("Name: ", Label.RIGHT));
+ tmp.add(name);
- }
- }
+ tmp = new Panel();
+ panel.add(tmp);
+ tmp.add(new Label("Group: ", Label.RIGHT));
+ tmp.add(source);
+
+ tmp = new Panel();
+ panel.add(tmp);
+ tmp.add(new Label("Colour: ", Label.RIGHT));
+ tmp.add(colourPanel);
+
+ bigPanel.add(panel, BorderLayout.NORTH);
- if (transparencySetter != null && g != null)
+ panel = new Panel();
+ panel.add(new Label("Description: ", Label.RIGHT));
+ panel.add(new ScrollPane().add(description));
+
+ if (!newFeatures)
{
- transparencySetter.setTransparency(g, 1.0f);
+ bigPanel.add(panel, BorderLayout.SOUTH);
+
+ panel = new Panel();
+ panel.add(new Label(" Start:", Label.RIGHT));
+ panel.add(start);
+ panel.add(new Label(" End:", Label.RIGHT));
+ panel.add(end);
+ bigPanel.add(panel, BorderLayout.CENTER);
+ }
+ else
+ {
+ bigPanel.add(panel, BorderLayout.CENTER);
}
- }
-
- char s;
- int i;
- void renderFeature(Graphics g, SequenceI seq,
- int fstart, int fend, Color featureColour, int start,
- int end, int y1)
- {
- if ( ( (fstart <= end) && (fend >= start)))
+ if (lastFeatureAdded == null)
{
- if (fstart < start)
- { // fix for if the feature we have starts before the sequence start,
- fstart = start; // but the feature end is still valid!!
+ if (features[0].type != null)
+ {
+ lastFeatureAdded = features[0].type;
}
-
- if (fend >= end)
+ else
{
- fend = end;
+ lastFeatureAdded = "feature_1";
}
+ }
- for (i = fstart; i <= fend; i++)
+ if (lastFeatureGroupAdded == null)
+ {
+ if (features[0].featureGroup != null)
{
- s = seq.getCharAt(i);
+ lastFeatureGroupAdded = features[0].featureGroup;
+ }
+ else
+ {
+ lastFeatureAdded = "Jalview";
+ }
+ }
- if (jalview.util.Comparison.isGap(s))
- {
- continue;
- }
+ String title = newFeatures ? MessageManager
+ .getString("label.create_new_sequence_features")
+ : MessageManager.formatMessage("label.amend_delete_features",
+ new String[] { sequences[0].getName() });
- g.setColor(featureColour);
+ final JVDialog dialog = new JVDialog(ap.alignFrame, title, true, 385,
+ 240);
- g.fillRect( (i - start) * av.charWidth, y1, av.charWidth, av.charHeight);
+ dialog.setMainPanel(bigPanel);
- if (!av.validCharWidth)
+ 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()
+ {
+ public void actionPerformed(ActionEvent evt)
{
- continue;
+ deleteFeature = true;
+ dialog.setVisible(false);
}
-
- g.setColor(Color.white);
- charOffset = (av.charWidth - fm.charWidth(s)) / 2;
- g.drawString(String.valueOf(s),
- charOffset + (av.charWidth * (i - start)),
- (y1 + av.charHeight) - av.charHeight / 5); //pady = height / 5;
-
- }
+ });
+ name.setText(features[0].getType());
+ source.setText(features[0].getFeatureGroup());
}
- }
- void findAllFeatures()
- {
- jalview.schemes.UserColourScheme ucs = new
- jalview.schemes.UserColourScheme();
-
- av.featuresDisplayed = new Hashtable();
- Vector allfeatures = new Vector();
- for (int i = 0; i < av.alignment.getHeight(); i++)
+ start.setText(features[0].getBegin() + "");
+ end.setText(features[0].getEnd() + "");
+ description.setText(features[0].getDescription());
+ Color col = getColour(name.getText());
+ if (col == null)
{
- SequenceFeature[] features = av.alignment.getSequenceAt(i).
- getSequenceFeatures();
-
- if (features == null)
- {
- continue;
- }
-
- int index = 0;
- while (index < features.length)
+ col = new jalview.schemes.UserColourScheme()
+ .createColourFromName(name.getText());
+ }
+ Object 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 java.awt.event.MouseAdapter()
+ {
+ public void mousePressed(java.awt.event.MouseEvent evt)
{
- if (!av.featuresDisplayed.containsKey(features[index].getType()))
+ if (!colourPanel.isGcol)
{
- if (getColour(features[index].getType()) == null)
- {
- featureColours.put(features[index].getType(),
- ucs.createColourFromName(features[index].
- getType()));
- }
-
- av.featuresDisplayed.put(features[index].getType(),
- new Integer(getColour(features[index].
- getType()).getRGB()));
- allfeatures.addElement(features[index].getType());
+ new UserDefinedColours(fr, ap.alignFrame);
+ }
+ else
+ {
+ FeatureColourChooser fcc = new FeatureColourChooser(
+ ap.alignFrame, name.getText());
+ dialog.transferFocus();
}
- index++;
}
- }
+ });
+ dialog.setVisible(true);
+
+ jalview.io.FeaturesFile ffile = new jalview.io.FeaturesFile();
- renderOrder = new String[allfeatures.size()];
- Enumeration en = allfeatures.elements();
- int i = allfeatures.size() - 1;
- while (en.hasMoreElements())
+ if (dialog.accept)
{
- renderOrder[i] = en.nextElement().toString();
- i--;
+ // 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', ' ');
}
- }
-
- public Color getColour(String featureType)
- {
- return (Color) featureColours.get(featureType);
- }
-
- public void addNewFeature(String name, Color col)
- {
- setColour(name, col);
- if (av.featuresDisplayed == null)
+ if (lastFeatureGroupAdded != null && lastFeatureGroupAdded.length() < 1)
{
- av.featuresDisplayed = new Hashtable();
+ lastFeatureGroupAdded = null;
}
- av.featuresDisplayed.put(name, "NOGROUP");
- }
-
- public void setColour(String featureType, Color col)
- {
- featureColours.put(featureType, col);
- }
-
- public void setFeaturePriority(Object[][] data)
- {
- // The feature table will display high priority
- // features at the top, but theses are the ones
- // we need to render last, so invert the data
- if (av.featuresDisplayed != null)
+ if (!newFeatures)
{
- av.featuresDisplayed.clear();
- }
- renderOrder = new String[data.length];
+ 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, 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);
+ }
- if (data.length > 0)
+ }
+ else
{
- for (int i = 0; i < data.length; i++)
+ if (dialog.accept && name.getText().length() > 0)
{
- String type = data[i][0].toString();
- setColour(type, (Color) data[i][1]);
- if ( ( (Boolean) data[i][2]).booleanValue())
+ for (int i = 0; i < sequences.length; i++)
{
- av.featuresDisplayed.put(type, new Integer(getColour(type).getRGB()));
+ features[i].type = lastFeatureAdded;
+ features[i].featureGroup = lastFeatureGroupAdded;
+ features[i].description = lastDescriptionAdded;
+ sequences[i].addSequenceFeature(features[i]);
+ ffile.parseDescriptionHTML(features[i], false);
}
- renderOrder[data.length - i - 1] = type;
+ Color newColour = colourPanel.getBackground();
+ // setColour(lastFeatureAdded, fcol);
+
+ if (lastFeatureGroupAdded != null)
+ {
+ setGroupVisibility(lastFeatureGroupAdded, true);
+ }
+ setColour(lastFeatureAdded, 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();
- public void featuresAdded()
- {
- findAllFeatures();
- }
-}
+ ap.paintAlignment(true);
-class TransparencySetter
-{
- void setTransparency(Graphics g, float value)
- {
- Graphics2D g2 = (Graphics2D) g;
- g2.setComposite(
- AlphaComposite.getInstance(
- AlphaComposite.SRC_OVER, value));
+ return true;
}
}
git://source.jalview.org / jalview.git / blobdiff