/*\r
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)\r
- * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)\r
+ * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, 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
+ * This file is part of Jalview.\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
+ * Jalview 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 3 of the License, or (at your option) any later version.\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
+ * Jalview is distributed in the hope that it will be useful, but \r
+ * WITHOUT ANY WARRANTY; without even the implied warranty \r
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR \r
+ * PURPOSE. See the GNU General Public License for more details.\r
+ * \r
+ * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.\r
*/\r
package jalview.gui;\r
\r
import java.util.*;\r
+import java.util.List;\r
\r
import java.awt.*;\r
import java.awt.event.*;\r
\r
AlignmentAnnotation[] annotations;\r
\r
- Vector sequenceGroups;\r
+ List<SequenceGroup> sequenceGroups;\r
\r
Hashtable alignmentProperties;\r
\r
frame = new JInternalFrame();\r
frame.setContentPane(this);\r
frame.setLayer(JLayeredPane.PALETTE_LAYER);\r
- Desktop.addInternalFrame(frame, "", 260, 125);\r
+ Desktop.addInternalFrame(frame, "", frame.getPreferredSize().width,\r
+ frame.getPreferredSize().height);\r
}\r
\r
public void exportFeatures(AlignmentPanel ap)\r
}\r
\r
public void exportAnnotations(AlignmentPanel ap,\r
- AlignmentAnnotation[] annotations, Vector sequenceGroups,\r
+ AlignmentAnnotation[] annotations, List<SequenceGroup> list,\r
Hashtable alProperties)\r
{\r
this.ap = ap;\r
GFFFormat.setVisible(false);\r
CSVFormat.setVisible(true);\r
this.annotations = annotations;\r
- this.sequenceGroups = sequenceGroups;\r
+ this.sequenceGroups = list;\r
this.alignmentProperties = alProperties;\r
frame.setTitle("Export Annotations");\r
}\r
\r
public void toFile_actionPerformed(ActionEvent e)\r
{\r
- JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache\r
- .getProperty("LAST_DIRECTORY"));\r
+ JalviewFileChooser chooser = new JalviewFileChooser(\r
+ jalview.bin.Cache.getProperty("LAST_DIRECTORY"));\r
\r
chooser.setFileView(new JalviewFileView());\r
chooser.setDialogTitle(features ? "Save Features to File"\r
{\r
if (GFFFormat.isSelected())\r
{\r
- text = new FeaturesFile().printGFFFormat(ap.av.alignment\r
+ text = new FeaturesFile().printGFFFormat(ap.av.getAlignment()\r
.getDataset().getSequencesArray(),\r
- getDisplayedFeatureCols());//ap.av.featuresDisplayed//);\r
+ getDisplayedFeatureCols(), true, ap.av.isShowNpFeats());// ap.av.featuresDisplayed//);\r
}\r
else\r
{\r
- text = new FeaturesFile().printJalviewFormat(ap.av.alignment\r
+ text = new FeaturesFile().printJalviewFormat(ap.av.getAlignment()\r
.getDataset().getSequencesArray(),\r
- getDisplayedFeatureCols()); // ap.av.featuresDisplayed);\r
+ getDisplayedFeatureCols(), true, ap.av.isShowNpFeats()); // ap.av.featuresDisplayed);\r
}\r
}\r
else\r
{\r
if (GFFFormat.isSelected())\r
{\r
- text = new FeaturesFile().printGFFFormat(ap.av.alignment\r
- .getDataset().getSequencesArray(), getDisplayedFeatureCols());\r
+ text = new FeaturesFile().printGFFFormat(ap.av.getAlignment()\r
+ .getDataset().getSequencesArray(),\r
+ getDisplayedFeatureCols(), true, ap.av.isShowNpFeats());\r
}\r
else\r
{\r
- text = new FeaturesFile().printJalviewFormat(ap.av.alignment\r
- .getDataset().getSequencesArray(), getDisplayedFeatureCols());\r
+ text = new FeaturesFile().printJalviewFormat(ap.av.getAlignment()\r
+ .getDataset().getSequencesArray(),\r
+ getDisplayedFeatureCols(), true, ap.av.isShowNpFeats());\r
}\r
}\r
else if (!features)\r
}\r
\r
CutAndPasteTransfer cap = new CutAndPasteTransfer();\r
- cap.setText(text);\r
- Desktop.addInternalFrame(cap, (features ? "Features for - "\r
- : "Annotations for - ")\r
- + ap.alignFrame.getTitle(), 600, 500);\r
+ try\r
+ {\r
+ cap.setText(text);\r
+ Desktop.addInternalFrame(cap, (features ? "Features for - "\r
+ : "Annotations for - ") + ap.alignFrame.getTitle(), 600, 500);\r
+ } catch (OutOfMemoryError oom)\r
+ {\r
+ new OOMWarning("generating "\r
+ + (features ? "Features for - " : "Annotations for - ")\r
+ + ap.alignFrame.getTitle(), oom);\r
+ cap.dispose();\r
+ }\r
\r
close_actionPerformed(null);\r
}\r
private Hashtable getDisplayedFeatureCols()\r
{\r
Hashtable fcols = new Hashtable();\r
+ if (ap.av.featuresDisplayed == null)\r
+ {\r
+ return fcols;\r
+ }\r
Enumeration en = ap.av.featuresDisplayed.keys();\r
- FeatureRenderer fr = ap.seqPanel.seqCanvas.getFeatureRenderer(); // consider higher level method ?\r
+ FeatureRenderer fr = ap.seqPanel.seqCanvas.getFeatureRenderer(); // consider\r
+ // higher\r
+ // level\r
+ // method ?\r
while (en.hasMoreElements())\r
{\r
Object col = en.nextElement();\r
\r
private void jbInit() throws Exception\r
{\r
- this.setLayout(flowLayout1);\r
+ this.setLayout(new BorderLayout());\r
+\r
toFile.setText("to File");\r
toFile.addActionListener(new ActionListener()\r
{\r
buttonGroup.add(jalviewFormat);\r
buttonGroup.add(GFFFormat);\r
buttonGroup.add(CSVFormat);\r
- this.add(jPanel3, null);\r
- this.add(jPanel1, null);\r
+ this.add(jPanel3, BorderLayout.CENTER);\r
+ this.add(jPanel1, BorderLayout.SOUTH);\r
}\r
\r
JPanel jPanel1 = new JPanel();\r
git://source.jalview.org / jalview.git / blobdiff