*/
package jalview.io;
+import java.io.File;
+import java.io.IOException;
+import java.util.StringTokenizer;
+import java.util.Vector;
+
+import javax.swing.SwingUtilities;
+
import jalview.api.ComplexAlignFile;
import jalview.api.FeatureSettingsModelI;
import jalview.api.FeaturesDisplayedI;
import jalview.util.MessageManager;
import jalview.ws.utils.UrlDownloadClient;
-import java.io.File;
-import java.io.IOException;
-import java.util.StringTokenizer;
-import java.util.Vector;
-
-import javax.swing.SwingUtilities;
+import java.util.ArrayList;
+import java.util.List;
public class FileLoader implements Runnable
{
+ private static final String TAB = "\t";
+
String file;
DataSourceType protocol;
boolean raiseGUI = true;
+ private File selectedFile;
+
/**
* default constructor always raised errors in GUI dialog boxes
*/
this.raiseGUI = raiseGUI;
}
- public void LoadFile(AlignViewport viewport, String file,
+ public void LoadFile(AlignViewport viewport, Object file,
DataSourceType protocol, FileFormatI format)
{
this.viewport = viewport;
- LoadFile(file, protocol, format);
+ if (file instanceof File) {
+ this.selectedFile = (File) file;
+ file = selectedFile.getPath();
+ }
+ LoadFile(file.toString(), protocol, format);
}
public void LoadFile(String file, DataSourceType protocol,
}
/**
+ * Load alignment from (file, protocol) of type format and wait till loaded
+ *
+ * @param file
+ * @param sourceType
+ * @param format
+ * @return alignFrame constructed from file contents
+ */
+ public AlignFrame LoadFileWaitTillLoaded(File file,
+ DataSourceType sourceType, FileFormatI format)
+ {
+ this.selectedFile = file;
+ this.file = file.getPath();
+ this.protocol = sourceType;
+ this.format = format;
+ return _LoadFileWaitTillLoaded();
+ }
+
+ /**
* Load alignment from FileParse source of type format and wait till loaded
*
* @param source
}
/**
- * start thread and wait until finished, then return the alignFrame that's
- * (hopefully) been read.
+ * runs the 'run' method (in this thread), then return the alignFrame that's
+ * (hopefully) been read
*
* @return
*/
protected AlignFrame _LoadFileWaitTillLoaded()
{
- Thread loader = new Thread(this);
- loader.start();
-
- while (loader.isAlive())
- {
- try
- {
- Thread.sleep(500);
- } catch (Exception ex)
- {
- System.out.println(
- "Exception caught while waiting for FileLoader thread");
- ex.printStackTrace();
- }
- }
+ this.run();
return alignFrame;
}
- public void updateRecentlyOpened()
+ public void LoadFileOntoAlignmentWaitTillLoaded(AlignViewport viewport,
+ String file, DataSourceType sourceType, FileFormatI format)
{
- Vector recent = new Vector();
+ Vector<String> recent = new Vector<>();
if (protocol == DataSourceType.PASTE)
+ this.viewport = viewport;
+ this.file = file;
+ this.protocol = sourceType;
+ this.format = format;
+ _LoadFileWaitTillLoaded();
+ }
+
+
+ /**
+ * 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)
+ {
+ 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();
+ 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
format = new IdentifyFile().identify(source, false);
// identify stream and rewind rather than close
}
+ else if (selectedFile != null) {
+ format = new IdentifyFile().identify(selectedFile, protocol);
+ }
else
{
format = new IdentifyFile().identify(file, protocol);
"IMPLEMENTATION ERROR: Cannot read consecutive Jalview XML projects from a stream.");
// We read the data anyway - it might make sense.
}
- alignFrame = new Jalview2XML(raiseGUI).loadJalviewAlign(file);
+ // BH 2018 switch to File object here instead of filename
+ alignFrame = new Jalview2XML(raiseGUI).loadJalviewAlign(selectedFile == null ? file : selectedFile);
}
else
{
file.lastIndexOf("."));
String tempStructureFileStr = createNamedJvTempFile(
urlLeafName, structExt);
- UrlDownloadClient.download(file, tempStructureFileStr);
- al = fa.readFile(tempStructureFileStr, DataSourceType.FILE,
+
+ // BH - switching to File object here so as to hold
+ // ._bytes array directly
+ File tempFile = new File(tempStructureFileStr);
+ UrlDownloadClient.download(file, tempFile);
+
+ al = fa.readFile(tempFile, DataSourceType.FILE,
format);
source = fa.getAlignFile();
}
else
{
- al = fa.readFile(file, protocol, format);
+ if (selectedFile == null) {
+ al = fa.readFile(file, protocol, format);
+
+ } else {
+ al = fa.readFile(selectedFile, protocol, format);
+ }
source = fa.getAlignFile(); // keep reference for later if
+
// necessary.
}
}
}
// append to existing alignment
viewport.addAlignment(al, title);
+ if (source instanceof HMMFile)
+ {
+ AlignmentI alignment = viewport.getAlignment();
+ SequenceI seq = alignment
+ .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.getAlignPanel().adjustAnnotationHeight();
+ viewport.updateSequenceIdColours();
+ }
}
else
{
if (!(protocol == DataSourceType.PASTE))
{
alignFrame.setFileName(file, format);
+ alignFrame.setFileObject(selectedFile); // BH 2018 SwingJS
}
if (proxyColourScheme != null)
{
}
}
- updateRecentlyOpened();
+ updateRecentlyOpened(file, protocol);
+
+ if (protocol == DataSourceType.FILE && format != null)
+ {
+ Cache.setProperty("DEFAULT_FILE_FORMAT", format.getName());
+ }
} catch (Exception er)
{