import jalview.datamodel.AlignmentI;
import jalview.datamodel.HiddenColumns;
import jalview.datamodel.PDBEntry;
-import jalview.datamodel.Profile;
-import jalview.datamodel.Profiles;
-import jalview.datamodel.SequenceGroup;
import jalview.datamodel.SequenceI;
import jalview.gui.AlignFrame;
import jalview.gui.AlignViewport;
import jalview.gui.Desktop;
-import jalview.gui.Jalview2XML;
import jalview.gui.JvOptionPane;
import jalview.json.binding.biojson.v1.ColourSchemeMapper;
+import jalview.project.Jalview2XML;
import jalview.schemes.ColourSchemeI;
import jalview.structure.StructureSelectionManager;
import jalview.util.MessageManager;
import java.io.File;
import java.io.IOException;
+import java.util.ArrayList;
+import java.util.List;
import java.util.StringTokenizer;
-import java.util.Vector;
import javax.swing.SwingUtilities;
public class FileLoader implements Runnable
{
+ private static final String TAB = "\t";
+
String file;
DataSourceType protocol;
Thread.sleep(500);
} catch (Exception ex)
{
+ System.out.println(
+ "Exception caught while waiting for FileLoader thread");
+ ex.printStackTrace();
}
}
}
}
- public void updateRecentlyOpened()
+ /**
+ * Updates (or creates) the tab-separated list of recently opened files held
+ * under the given property name by inserting the filePath at the front of the
+ * list. Duplicates are removed, and the list is limited to 11 entries. The
+ * method returns the updated value of the property.
+ *
+ * @param filePath
+ * @param sourceType
+ */
+ public static String updateRecentlyOpened(String filePath,
+ DataSourceType sourceType)
{
- Vector recent = new Vector();
- if (protocol == DataSourceType.PASTE)
+ if (sourceType != DataSourceType.FILE
+ && sourceType != DataSourceType.URL)
{
- // do nothing if the file was pasted in as text... there is no filename to
- // refer to it as.
- return;
+ return null;
}
- if (file != null
- && file.indexOf(System.getProperty("java.io.tmpdir")) > -1)
+
+ String propertyName = sourceType == DataSourceType.FILE ? "RECENT_FILE"
+ : "RECENT_URL";
+ String historyItems = Cache.getProperty(propertyName);
+ if (filePath != null
+ && filePath.indexOf(System.getProperty("java.io.tmpdir")) > -1)
{
// ignore files loaded from the system's temporary directory
- return;
+ return null;
}
- String type = protocol == DataSourceType.FILE ? "RECENT_FILE"
- : "RECENT_URL";
-
- String historyItems = jalview.bin.Cache.getProperty(type);
- StringTokenizer st;
+ List<String> recent = new ArrayList<>();
if (historyItems != null)
{
- st = new StringTokenizer(historyItems, "\t");
+ StringTokenizer st = new StringTokenizer(historyItems, TAB);
while (st.hasMoreTokens())
{
- recent.addElement(st.nextElement().toString().trim());
+ String trimmed = st.nextToken().trim();
+ if (!recent.contains(trimmed))
+ {
+ recent.add(trimmed);
+ }
}
}
- if (recent.contains(file))
+ /*
+ * if file was already in the list, it moves to the top
+ */
+ if (recent.contains(filePath))
{
- recent.remove(file);
+ recent.remove(filePath);
}
- StringBuffer newHistory = new StringBuffer(file);
+ StringBuilder newHistory = new StringBuilder(filePath);
for (int i = 0; i < recent.size() && i < 10; i++)
{
- newHistory.append("\t");
- newHistory.append(recent.elementAt(i));
+ newHistory.append(TAB);
+ newHistory.append(recent.get(i));
}
- Cache.setProperty(type, newHistory.toString());
+ String newProperty = newHistory.toString();
+ Cache.setProperty(propertyName, newProperty);
- if (protocol == DataSourceType.FILE)
- {
- Cache.setProperty("DEFAULT_FILE_FORMAT", format.getName());
- }
+ return newProperty;
}
@Override
viewport.addAlignment(al, title);
if (source instanceof HMMFile)
{
+ // TODO: absorb into viewport.addAlignment above ?
AlignmentI alignment = viewport.getAlignment();
SequenceI seq = alignment
- .getSequenceAt(alignment.getAbsoluteHeight() - 1);
- alignment.deleteSequence(alignment.getAbsoluteHeight() - 1);
- SequenceGroup sg = viewport.getSelectionGroup();
- if (sg != null)
- {
- seq.insertCharAt(0, sg.getStartRes(), '-');
- seq.insertCharAt(sg.getEndRes() + 1,
- alignment.getWidth() - sg.getEndRes(), '-');
- SequenceI topSeq = sg.getSequencesInOrder(alignment)[0];
- int topIndex = alignment.findIndex(topSeq);
- alignment.insertSequenceAt(topIndex, seq);
- sg.setSeqrep(seq);
- viewport.getSelectionGroup().addSequence(seq, false);
- }
- else
+ .getSequenceAt(alignment.getHeight() - 1);
+ if (seq.hasHMMProfile())
{
+ /*
+ * fudge: move HMM consensus sequence from last to first
+ */
+ alignment.deleteSequence(alignment.getAbsoluteHeight() - 1);
alignment.insertSequenceAt(0, seq);
}
- viewport.initInformation();
- viewport.setSequenceInformationHash(
- new Profiles(new Profile[1]), 0);
- viewport.updateInformation(viewport.getAlignPanel());
viewport.getAlignPanel().adjustAnnotationHeight();
viewport.updateSequenceIdColours();
- if (viewport.getAlignPanel().alignFrame
- .getSelectedHMM() == null)
+ // update HMM colour options
+ if (alignFrame != null)
{
- viewport.getAlignPanel().alignFrame
- .setSelectedHMM(seq.getHMM());
+ alignFrame.buildColourMenu();
}
-
}
}
else
alignFrame.getViewport()
.applyFeaturesStyle(proxyColourScheme);
}
- alignFrame.statusBar.setText(MessageManager.formatMessage(
+ alignFrame.setStatus(MessageManager.formatMessage(
"label.successfully_loaded_file", new String[]
{ title }));
}
}
- updateRecentlyOpened();
+ updateRecentlyOpened(file, protocol);
+
+ if (protocol == DataSourceType.FILE && format != null)
+ {
+ Cache.setProperty("DEFAULT_FILE_FORMAT", format.getName());
+ }
} catch (Exception er)
{
return tempStructFile.toString();
}
- /*
- * (non-Javadoc)
- *
- * @see java.lang.Object#finalize()
- */
- @Override
- protected void finalize() throws Throwable
- {
- source = null;
- alignFrame = null;
- viewport = null;
- super.finalize();
- }
-
}
git://source.jalview.org / jalview.git / blobdiff