*/
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.gui.AlignViewport;
import jalview.gui.BamFileOptionsChooser;
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 jalview.ws.utils.UrlDownloadClient;
-import java.io.File;
-import java.io.IOException;
-import java.util.StringTokenizer;
-import java.util.Vector;
-
-import javax.swing.SwingUtilities;
-
public class FileLoader implements Runnable
{
String file;
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)
- {
- }
- }
+ this.run();
return alignFrame;
}
public void updateRecentlyOpened()
{
- Vector recent = new Vector();
+ Vector<String> recent = new Vector<>();
if (protocol == DataSourceType.PASTE)
{
// do nothing if the file was pasted in as text... there is no filename to
String type = protocol == DataSourceType.FILE ? "RECENT_FILE"
: "RECENT_URL";
- String historyItems = jalview.bin.Cache.getProperty(type);
+ String historyItems = Cache.getProperty(type);
StringTokenizer st;
while (st.hasMoreTokens())
{
- recent.addElement(st.nextElement().toString().trim());
+ recent.addElement(st.nextToken().trim());
}
}
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);
FormatAdapter fa = new FormatAdapter();
if (source == null)
{
- fa.prepareFileReader(file, protocol, format);
+ fa.prepareFileReader(null, file, protocol, format);
source = fa.getAlignFile();
}
if (!((BamFile) source).parseSuffix())
"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
{
String error = AppletFormatAdapter.getSupportedFormats();
try
{
- if (al == null)
+ if (source != null)
{
- if (source != null)
+ // read from the provided source
+ al = new FormatAdapter().readFromFile(source, format);
+ }
+ else
+ {
+
+ // open a new source and read from it
+ FormatAdapter fa = new FormatAdapter();
+ boolean downloadStructureFile = format.isStructureFile()
+ && protocol.equals(DataSourceType.URL);
+ if (downloadStructureFile)
{
- // read from the provided source
- al = new FormatAdapter().readFromFile(source, format);
+ String structExt = format.getExtensions().split(",")[0];
+ String urlLeafName = file.substring(
+ file.lastIndexOf(
+ System.getProperty("file.separator")),
+ file.lastIndexOf("."));
+ String tempStructureFileStr = createNamedJvTempFile(
+ urlLeafName, structExt);
+
+ // 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
{
-
- // open a new source and read from it
- FormatAdapter fa = new FormatAdapter();
- boolean downloadStructureFile = format.isStructureFile()
- && protocol.equals(DataSourceType.URL);
- if (downloadStructureFile)
- {
- String structExt = format.getExtensions().split(",")[0];
- String urlLeafName = file.substring(
- file.lastIndexOf(
- System.getProperty("file.separator")),
- file.lastIndexOf("."));
- String tempStructureFileStr = createNamedJvTempFile(
- urlLeafName, structExt);
- UrlDownloadClient.download(file, tempStructureFileStr);
- al = fa.readFile(tempStructureFileStr, DataSourceType.FILE,
- format);
- source = fa.getAlignFile();
- }
- else
- {
+ if (selectedFile == null) {
al = fa.readFile(file, protocol, format);
- source = fa.getAlignFile(); // keep reference for later if
- // necessary.
- }
+
+ } else {
+ al = fa.readFile(selectedFile, protocol, format);
+ }
+ source = fa.getAlignFile(); // keep reference for later if
+ // necessary.
}
}
} catch (java.io.IOException ex)
.getFeatureColourScheme();
if (viewport != null)
{
- if (proxyColourScheme != null)
- {
- viewport.applyFeaturesStyle(proxyColourScheme);
- }
// append to existing alignment
viewport.addAlignment(al, title);
+ viewport.applyFeaturesStyle(proxyColourScheme);
}
else
{
if (!(protocol == DataSourceType.PASTE))
{
alignFrame.setFileName(file, format);
+ alignFrame.setFileObject(selectedFile); // BH 2018 SwingJS
}
if (proxyColourScheme != null)
{
alignFrame.getViewport()
.applyFeaturesStyle(proxyColourScheme);
}
- alignFrame.statusBar.setText(MessageManager.formatMessage(
+ alignFrame.setStatus(MessageManager.formatMessage(
"label.successfully_loaded_file", new String[]
{ title }));
git://source.jalview.org / jalview.git / blobdiff