/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2b1)
+ * Copyright (C) 2014 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.
- *
+ * 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/>.
+ * 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 java.awt.event.*;
-import jalview.appletgui.FeatureSettings.MyCheckbox;
import jalview.datamodel.*;
import jalview.schemes.AnnotationColourGradient;
import jalview.schemes.GraduatedColor;
+import jalview.util.MessageManager;
/**
* DOCUMENT ME!
featureGroups = fr.featureGroups;
featureColours = fr.featureColours;
transparency = fr.transparency;
+ if (av != null && fr.av != null && fr.av != av)
+ {
+ if (fr.av.featuresDisplayed != null)
+ {
+ if (av.featuresDisplayed == null)
+ {
+ av.featuresDisplayed = new Hashtable();
+ }
+ else
+ {
+ av.featuresDisplayed.clear();
+ }
+ Enumeration en = fr.av.featuresDisplayed.keys();
+ while (en.hasMoreElements())
+ {
+ av.featuresDisplayed.put(en.nextElement(), Boolean.TRUE);
+ }
+ }
+ }
}
static String lastFeatureAdded;
}
else
{
- throw new Error("Invalid color for MyCheckBox");
+ throw new Error(MessageManager.getString("error.invalid_colour_for_mycheckbox"));
}
if (col != null)
{
g.setColor(Color.black);
Font f = new Font("Verdana", Font.PLAIN, 10);
g.setFont(f);
- g.drawString("Label", 0, 0);
+ g.drawString(MessageManager.getString("label.label"), 0, 0);
}
else
{
}
}
- String title = newFeatures ? "Create New Sequence Feature(s)"
- : "Amend/Delete Features for " + sequences[0].getName();
+ 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);
}
else
{
- dialog.ok.setLabel("Amend");
+ dialog.ok.setLabel(MessageManager.getString("label.amend"));
dialog.buttonPanel.add(deleteButton, 1);
deleteButton.addActionListener(new ActionListener()
{
else if (sequenceFeatures[sfindex].type.equals("disulfide bond"))
{
- renderFeature(g, seq, seq
- .findIndex(sequenceFeatures[sfindex].begin) - 1, seq
- .findIndex(sequenceFeatures[sfindex].begin) - 1,
+ renderFeature(g, seq,
+ seq.findIndex(sequenceFeatures[sfindex].begin) - 1,
+ seq.findIndex(sequenceFeatures[sfindex].begin) - 1,
getColour(sequenceFeatures[sfindex])
// 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,
+ renderFeature(g, seq,
+ seq.findIndex(sequenceFeatures[sfindex].end) - 1,
+ seq.findIndex(sequenceFeatures[sfindex].end) - 1,
getColour(sequenceFeatures[sfindex])
// new Color(((Integer) av.featuresDisplayed
// .get(sequenceFeatures[sfindex].type)).intValue())
{
if (showFeature(sequenceFeatures[sfindex]))
{
- renderFeature(g, seq, seq
- .findIndex(sequenceFeatures[sfindex].begin) - 1, seq
- .findIndex(sequenceFeatures[sfindex].end) - 1,
+ renderFeature(g, seq,
+ seq.findIndex(sequenceFeatures[sfindex].begin) - 1,
+ seq.findIndex(sequenceFeatures[sfindex].end) - 1,
getColour(sequenceFeatures[sfindex]), start, end, y1);
}
}
}
Hashtable minmax = null;
+
/**
* Called when alignment in associated view has new/modified features to
* discover and display.
lastSeq = null;
findAllFeatures();
}
+
/**
* find all features on the alignment
*/
av.featuresDisplayed = new Hashtable();
Vector allfeatures = new Vector();
minmax = new Hashtable();
-
- for (int i = 0; i < av.alignment.getHeight(); i++)
+ AlignmentI alignment = av.getAlignment();
+ for (int i = 0; i < alignment.getHeight(); i++)
{
- SequenceFeature[] features = av.alignment.getSequenceAt(i)
+ SequenceFeature[] features = alignment.getSequenceAt(i)
.getSequenceFeatures();
if (features == null)
{
if (getColour(features[index].getType()) == null)
{
- featureColours.put(features[index].getType(), ucs
- .createColourFromName(features[index].getType()));
+ featureColours.put(features[index].getType(),
+ ucs.createColourFromName(features[index].getType()));
}
av.featuresDisplayed.put(features[index].getType(), new Integer(
return ((GraduatedColor) fc).getMaxColor();
}
}
- throw new Error("Implementation Error: Unrecognised render object "
- + fc.getClass() + " for features of type " + featureType);
+ throw new Error(MessageManager.formatMessage("error.implementation_error_unrecognised_render_object_for_features_type", new String[]{fc.getClass().getCanonicalName(),featureType}));
}
/**
for (int i = 0; i < toset.length; i++)
{
Object st = featureGroups.get(toset[i]);
+ featureGroups.put(toset[i], new Boolean(visible));
if (st != null)
{
- featureGroups.put(toset[i], new Boolean(visible));
rdrw = rdrw || (visible != ((Boolean) st).booleanValue());
}
}
}
}
+ ArrayList<String> hiddenGroups = new ArrayList<String>();
+
/**
* analyse alignment for groups and hash tables (used to be embedded in
* FeatureSettings.setTableData)
{
featureGroups = new Hashtable();
}
- Vector allFeatures = new Vector();
- Vector allGroups = new Vector();
+ hiddenGroups = new ArrayList<String>();
+ hiddenGroups.addAll(featureGroups.keySet());
+ ArrayList allFeatures = new ArrayList();
+ ArrayList allGroups = new ArrayList();
SequenceFeature[] tmpfeatures;
String group;
- for (int i = 0; i < av.alignment.getHeight(); i++)
+ AlignmentI alignment = av.getAlignment();
+ for (int i = 0; i < alignment.getHeight(); i++)
{
- if (av.alignment.getSequenceAt(i).getSequenceFeatures() == null)
+ if (alignment.getSequenceAt(i).getSequenceFeatures() == null)
{
continue;
}
alignmentHasFeatures = true;
- tmpfeatures = av.alignment.getSequenceAt(i).getSequenceFeatures();
+ tmpfeatures = alignment.getSequenceAt(i).getSequenceFeatures();
int index = 0;
while (index < tmpfeatures.length)
{
if (tmpfeatures[index].getFeatureGroup() != null)
{
group = tmpfeatures[index].featureGroup;
+ // Remove group from the hiddenGroup list
+ hiddenGroups.remove(group);
if (!allGroups.contains(group))
{
- allGroups.addElement(group);
+ allGroups.add(group);
boolean visible = true;
if (featureGroups.containsKey(group))
if (!allFeatures.contains(tmpfeatures[index].getType()))
{
- allFeatures.addElement(tmpfeatures[index].getType());
+ allFeatures.add(tmpfeatures[index].getType());
}
index++;
}
Vector allFeatures = new Vector();
SequenceFeature[] tmpfeatures;
String group;
- for (int i = 0; i < av.alignment.getHeight(); i++)
+ AlignmentI alignment = av.getAlignment();
+ for (int i = 0; i < alignment.getHeight(); i++)
{
- if (av.alignment.getSequenceAt(i).getSequenceFeatures() == null)
+ if (alignment.getSequenceAt(i).getSequenceFeatures() == null)
{
continue;
}
alignmentHasFeatures = true;
- tmpfeatures = av.alignment.getSequenceAt(i).getSequenceFeatures();
+ tmpfeatures = alignment.getSequenceAt(i).getSequenceFeatures();
int index = 0;
while (index < tmpfeatures.length)
{
git://source.jalview.org / jalview.git / blobdiff