/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* 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.gui;
if (GFFFormat.isSelected())
{
text = new FeaturesFile().printGFFFormat(ap.av.getAlignment()
- .getDataset().getSequencesArray(),
- getDisplayedFeatureCols(), true, ap.av.isShowNpFeats());// ap.av.featuresDisplayed//);
+ .getDataset().getSequencesArray(), ap
+ .getFeatureRenderer().getDisplayedFeatureCols(), true,
+ ap.av.isShowNpFeats());// ap.av.featuresDisplayed//);
}
else
{
text = new FeaturesFile().printJalviewFormat(ap.av.getAlignment()
- .getDataset().getSequencesArray(),
- getDisplayedFeatureCols(), true, ap.av.isShowNpFeats()); // ap.av.featuresDisplayed);
+ .getDataset().getSequencesArray(), ap
+ .getFeatureRenderer().getDisplayedFeatureCols(), true,
+ ap.av.isShowNpFeats()); // ap.av.featuresDisplayed);
}
}
else
if (GFFFormat.isSelected())
{
text = new FeaturesFile().printGFFFormat(ap.av.getAlignment()
- .getDataset().getSequencesArray(),
- getDisplayedFeatureCols(), true, ap.av.isShowNpFeats());
+ .getDataset().getSequencesArray(), ap.getFeatureRenderer()
+ .getDisplayedFeatureCols(), true, ap.av.isShowNpFeats());
}
else
{
text = new FeaturesFile().printJalviewFormat(ap.av.getAlignment()
- .getDataset().getSequencesArray(),
- getDisplayedFeatureCols(), true, ap.av.isShowNpFeats());
+ .getDataset().getSequencesArray(), ap.getFeatureRenderer()
+ .getDisplayedFeatureCols(), true, ap.av.isShowNpFeats());
}
}
else if (!features)
try
{
cap.setText(text);
- Desktop.addInternalFrame(cap, (features ? MessageManager.formatMessage("label.features_for_params", new String[]{ap.alignFrame.getTitle()})
- : MessageManager.formatMessage("label.annotations_for_params", new String[]{ap.alignFrame.getTitle()})), 600, 500);
+ Desktop.addInternalFrame(
+ cap,
+ (features ? MessageManager.formatMessage(
+ "label.features_for_params", new String[]
+ { ap.alignFrame.getTitle() }) : MessageManager
+ .formatMessage("label.annotations_for_params",
+ new String[]
+ { ap.alignFrame.getTitle() })), 600, 500);
} catch (OutOfMemoryError oom)
{
- new OOMWarning((features ? MessageManager.formatMessage("label.generating_features_for_params", new String[]{ap.alignFrame.getTitle()}) : MessageManager.formatMessage("label.generating_annotations_for_params", new String[]{ap.alignFrame.getTitle()}))
- , oom);
+ new OOMWarning((features ? MessageManager.formatMessage(
+ "label.generating_features_for_params", new String[]
+ { ap.alignFrame.getTitle() }) : MessageManager.formatMessage(
+ "label.generating_annotations_for_params", new String[]
+ { ap.alignFrame.getTitle() })), oom);
cap.dispose();
}
close_actionPerformed(null);
}
- private Hashtable getDisplayedFeatureCols()
- {
- Hashtable fcols = new Hashtable();
- if (ap.av.featuresDisplayed == null)
- {
- return fcols;
- }
- Enumeration en = ap.av.featuresDisplayed.keys();
- FeatureRenderer fr = ap.seqPanel.seqCanvas.getFeatureRenderer(); // consider
- // higher
- // level
- // method ?
- while (en.hasMoreElements())
- {
- Object col = en.nextElement();
- fcols.put(col, fr.featureColours.get(col));
- }
- return fcols;
- }
-
public void close_actionPerformed(ActionEvent e)
{
try