package jalview.bin;
+import jalview.analysis.AlignmentUtils;
+import jalview.datamodel.AlignmentI;
import jalview.gui.AlignFrame;
-import jalview.gui.Desktop;
-import jalview.io.AppletFormatAdapter;
+import jalview.gui.SplitFrame;
import jalview.io.DataSourceType;
import jalview.io.FileFormatException;
import jalview.io.FileFormatI;
import jalview.io.FileLoader;
import jalview.io.IdentifyFile;
+import jalview.structure.StructureSelectionManager;
import java.util.ArrayList;
import java.util.HashMap;
import java.util.List;
import java.util.Map;
-import java.util.Objects;
import javax.swing.JFrame;
+import javax.swing.JInternalFrame;
/**
* Entry point for Jalview as Javascript. Expects parameter names as for the
// TODO or format as file=/examples/uniref50.fa (etc)?
public class JalviewJS
{
+
+ static
+ {
+ /**
+ * @j2sNative
+ *
+ * thisApplet.__Info.args =
+ * ["file","examples/uniref50.fa","features",
+ * "examples/exampleFeatures.txt",
+ * "props","/Users/gmcarstairs/.jalview_properties"];
+ */
+
+ }
+
private static final String PARAM_FILE = "file";
private static final String PARAM_FILE2 = "file2";
private List<String> pdbFileParams;
- public static void main(String[] args)
+ public static void main(String[] args) throws Exception
{
- try
- {
- new JalviewJS().doMain(args);
- } catch (FileFormatException e)
- {
- e.printStackTrace();
- }
+ new JalviewJS().doMain(args);
}
/**
*/
private void usage()
{
- System.err.println("Usage: JalviewJS file <alignmentFile>");
+ System.err.println(
+ "Usage: JalviewJS file <alignmentFile> [features <featuresFile>]");
System.err.println("See documentation for full parameter list");
}
frame.setDefaultCloseOperation(JFrame.EXIT_ON_CLOSE);
/*
- * construct an AlignFrame and extract its contents and menu bar
+ * construct an AlignFrame (optionally with features)
+ */
+ AlignFrame alignFrame = createAlignFrame(PARAM_FILE);
+ loadFeatures(alignFrame, getParameter(PARAM_FEATURES));
+
+ JInternalFrame internalFrame = alignFrame;
+
+ /*
+ * convert to SplitFrame if a valid file2 is supplied
+ */
+ AlignFrame alignFrame2 = createAlignFrame(PARAM_FILE2);
+ if (alignFrame2 != null)
+ {
+ SplitFrame splitFrame = loadSplitFrame(alignFrame, alignFrame2);
+ if (splitFrame != null)
+ {
+ internalFrame = splitFrame;
+ }
+ }
+
+ /*
+ * move AlignFrame (or SplitFrame) menu bar and content pane to our frame
* TODO there may be a less obscure way to do this
*/
- AlignFrame alignFrame = createAlignFrame();
- frame.setContentPane(alignFrame.getContentPane());
- frame.setJMenuBar(alignFrame.getJMenuBar());
+ frame.setContentPane(internalFrame.getContentPane());
+ frame.setJMenuBar(internalFrame.getJMenuBar());
// fudge so that dialogs can be opened with this frame as parent
- Desktop.parent = frame.getContentPane();
-
- loadFeatures(alignFrame, getParameter(PARAM_FEATURES));
+ // todo JAL-3031 also override Desktop.addInternalFrame etc
+ // Desktop.parent = frame.getContentPane();
frame.pack();
frame.setSize(AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
}
/**
- * Load on a features file if one was specified as a parameter
+ * Constructs a SplitFrame if cdna-protein mappings can be made between the
+ * given alignment frames, else returns null. Any mappings made are registered
+ * with StructureSelectionManager to enable broadcast to listeners.
*
* @param alignFrame
+ * @param alignFrame2
+ * @return
+ */
+ protected SplitFrame loadSplitFrame(AlignFrame alignFrame,
+ AlignFrame alignFrame2)
+ {
+ // code borrowed from AlignViewport.openLinkedAlignment
+ AlignmentI al1 = alignFrame.getViewport().getAlignment();
+ AlignmentI al2 = alignFrame2.getViewport().getAlignment();
+ boolean al1Nuc = al1.isNucleotide();
+ if (al1Nuc == al2.isNucleotide())
+ {
+ System.err.println("Can't make split frame as alignments are both "
+ + (al1Nuc ? "nucleotide" : "protein"));
+ return null;
+ }
+ AlignmentI protein = al1Nuc ? al2 : al1;
+ AlignmentI cdna = al1Nuc ? al1 : al2;
+ boolean mapped = AlignmentUtils.mapProteinAlignmentToCdna(protein,
+ cdna);
+ if (!mapped)
+ {
+ System.err.println("Can't make any mappings for split frame");
+ return null;
+ }
+
+ /*
+ * register sequence mappings
+ */
+ StructureSelectionManager ssm = StructureSelectionManager
+ .getStructureSelectionManager(null);
+ ssm.registerMappings(protein.getCodonFrames());
+
+ cdna.alignAs(protein);
+
+ SplitFrame splitFrame = new SplitFrame(
+ al1Nuc ? alignFrame : alignFrame2,
+ al1Nuc ? alignFrame2 : alignFrame);
+
+ return splitFrame;
+ }
+
+ /**
+ * Loads on a features file if one was specified as a parameter
*
+ * @param alignFrame
* @param featureFile
*/
protected void loadFeatures(AlignFrame alignFrame, String featureFile)
// todo extract helper for protocol resolution from JalviewLite
DataSourceType sourceType = featureFile.startsWith("http")
? DataSourceType.URL
- : DataSourceType.FILE;
+ : DataSourceType.LOCALURL;
alignFrame.parseFeaturesFile(featureFile, sourceType);
}
}
/**
* Constructs and returns the frame containing the alignment and its
- * annotations
+ * annotations. Returns null if the specified parameter value is not set.
+ *
+ * @param fileParam
*
* @return
* @throws FileFormatException
*/
- AlignFrame createAlignFrame() throws FileFormatException
+ AlignFrame createAlignFrame(String fileParam) throws FileFormatException
{
- String file = getParameter(PARAM_FILE);
- Objects.requireNonNull(file);
-
- DataSourceType protocol = AppletFormatAdapter.checkProtocol(file);
- FileFormatI format = new IdentifyFile().identify(file, protocol);
- FileLoader fileLoader = new FileLoader(false);
- AlignFrame af = fileLoader.LoadFileWaitTillLoaded(file, protocol,
- format);
+ AlignFrame af = null;
+ String file = getParameter(fileParam);
+ if (file != null)
+ {
+ DataSourceType protocol = file.startsWith("http") ? DataSourceType.URL
+ : DataSourceType.LOCALURL;
+ // DataSourceType protocol = AppletFormatAdapter.checkProtocol(file);
+ FileFormatI format = new IdentifyFile().identify(file, protocol);
+ FileLoader fileLoader = new FileLoader(false);
+ af = fileLoader.LoadFileWaitTillLoaded(file, protocol, format);
+ }
return af;
}
git://source.jalview.org / jalview.git / blobdiff