import java.util.Map;
import jalview.analysis.AlignmentUtils;
+import jalview.api.AlignmentViewPanel;
import jalview.bin.ArgParser.Arg;
import jalview.bin.ArgParser.ArgValues;
import jalview.datamodel.AlignmentAnnotation;
import jalview.gui.AlignFrame;
+import jalview.gui.AlignViewport;
import jalview.gui.Desktop;
import jalview.io.AppletFormatAdapter;
import jalview.io.DataSourceType;
.getFirstSequenceAnnotationOfType(
af.getCurrentView().getAlignment(),
AlignmentAnnotation.LINE_GRAPH);
- Console.debug("***** Trying to change label from '"
- + (aa == null ? aa : aa.label) + "' to '"
- + m.get(Arg.TEMPFAC_LABEL).getValue() + "'");
if (aa != null)
{
aa.label = m.get(Arg.TEMPFAC_LABEL).getValue();
}
}
- //
-
- // load a pAE file?
- if (m.get(Arg.PAEMATRIX) != null)
- {
- File paeFile = new File(m.get(Arg.PAEMATRIX).getValue());
- EBIAlfaFold.addAlphaFoldPAE(af.getCurrentView().getAlignment(),
- paeFile);
- }
-
// store the AlignFrame for this id
afMap.put(id, af);
}
}
}
+
+ // load a pAE file if given
+ if (m.get(Arg.PAEMATRIX) != null)
+ {
+ AlignFrame af = afMap.get(id);
+ if (af != null)
+ {
+ for (String val : m.get(Arg.PAEMATRIX).getValues())
+ {
+ SubId subId = new SubId(val);
+ File paeFile = new File(subId.content);
+ EBIAlfaFold.addAlphaFoldPAE(af.getCurrentView().getAlignment(),
+ paeFile, subId.index,
+ "id".equals(subId.keyName) ? subId.keyValue : null);
+ // required to readjust the height and position of the pAE
+ // annotation
+ for (AlignmentViewPanel ap : af.getAlignPanels())
+ {
+ ap.adjustAnnotationHeight();
+ }
+ }
+ }
+ }
}
+ /**
+ * A helper class to parse a string of the possible forms "content"
+ * "[index]content", "[keyName=keyValue]content" and return the integer index,
+ * the strings keyName and keyValue, and the content after the square brackets
+ * (if present). Values not set will be -1 or null.
+ */
+ protected class SubId
+ {
+ protected int index = 0;
+
+ protected String keyName = null;
+
+ protected String keyValue = null;
+
+ protected String content = null;
+
+ protected SubId(String item)
+ {
+ if (item.indexOf('[') == 0 && item.indexOf(']') > 1)
+ {
+ int openBracket = item.indexOf('[');
+ int closeBracket = item.indexOf(']');
+ String indexString = item.substring(openBracket + 1, closeBracket);
+ this.content = item.substring(closeBracket + 1);
+ int equals = indexString.indexOf('=');
+ if (equals > -1)
+ {
+ this.keyName = indexString.substring(0, equals);
+ this.keyValue = indexString.substring(equals + 1);
+ this.index = -1;
+ }
+ else
+ {
+ try
+ {
+ this.index = Integer.parseInt(indexString);
+ } catch (NumberFormatException e)
+ {
+ Console.warn("Failed to obtain sequenced id or index from '"
+ + item + "'. Setting index=0 and using content='"
+ + content + "'.");
+ }
+ }
+ }
+ else
+ {
+ this.content = item;
+ }
+ }
+ }
+
+ private void testMethod()
+ {
+ Desktop Jalview = Desktop.instance;
+ jalview.bin.Cache.setProperty("SVG_RENDERING", "Text");
+ for (AlignFrame af : Jalview.getAlignFrames())
+ {
+ String title = af.getTitle();
+ System.out.println("Title: " + af.getTitle());
+ AlignViewport view = af.getCurrentView();
+ view.setShowText(false);
+ view.setShowAnnotation(false);
+ af.deselectAllSequenceMenuItem_actionPerformed(null);
+ af.repaint();
+ af.createPNG(new File(title + ".png"));
+ af.createSVG(new File(title + ".svg"));
+ }
+ }
}
Console.debug("Downloading pae from " + paeURL + " to " + pae.toString()
+ "");
UrlDownloadClient.download(paeURL, pae);
- addAlphaFoldPAE(pdbAlignment, pae);
+ addAlphaFoldPAE(pdbAlignment, pae, 0, null);
}
- public static void addAlphaFoldPAE(AlignmentI pdbAlignment, File pae)
+ public static void addAlphaFoldPAE(AlignmentI pdbAlignment, File pae,
+ int index, String seqId)
{
FileInputStream pae_input = null;
try
try
{
- if (!importPaeJSONAsContactMatrix(pdbAlignment, pae_input))
+ if (!importPaeJSONAsContactMatrix(pdbAlignment, pae_input, index,
+ seqId))
{
Console.warn("Could not import contact matrix from '"
+ pae.getAbsolutePath() + "'");
AlignmentI pdbAlignment, InputStream pae_input)
throws IOException, ParseException
{
+ return importPaeJSONAsContactMatrix(pdbAlignment, pae_input, 0, null);
+ }
+
+ public static boolean importPaeJSONAsContactMatrix(
+ AlignmentI pdbAlignment, InputStream pae_input, int index,
+ String seqId) throws IOException, ParseException
+ {
List<Object> pae_obj = (List<Object>) Platform.parseJSON(pae_input);
if (pae_obj == null)
{
+ Console.debug("JSON file did not parse properly.");
return false;
}
- ContactMatrixI matrix = new PAEContactMatrix(
- pdbAlignment.getSequenceAt(0),
+ SequenceI sequence = null;
+ /* debugging */
+ SequenceI[] seqs = pdbAlignment.getSequencesArray();
+ if (seqs == null)
+ Console.debug("******* sequences is null");
+ else
+ {
+ for (int i = 0; i < seqs.length; i++)
+ {
+ SequenceI s = seqs[i];
+ Console.debug("******* sequences[" + i + "]='" + s.getName() + "'");
+ }
+ }
+ /* end debug */
+ if (seqId == null)
+ {
+ int seqToGet = index > 0 ? index : 0;
+ sequence = pdbAlignment.getSequenceAt(seqToGet);
+ Console.debug("***** Got sequence at index " + seqToGet + ": "
+ + (sequence == null ? null : sequence.getName()));
+ }
+ else
+ {
+ Console.debug("***** Looking for sequence with id '" + seqId + "'");
+
+ SequenceI[] sequences = pdbAlignment.findSequenceMatch(seqId);
+ if (sequences == null || sequences.length < 1)
+ {
+ Console.warn("Could not find sequence with id '" + seqId
+ + "' to attach pAE matrix to. Ignoring matrix.");
+ return false;
+ }
+ else
+ {
+ sequence = sequences[0]; // just use the first sequence with this seqId
+ }
+ }
+ ContactMatrixI matrix = new PAEContactMatrix(sequence,
(Map<String, Object>) pae_obj.get(0));
- AlignmentAnnotation cmannot = pdbAlignment.getSequenceAt(0)
- .addContactList(matrix);
+ AlignmentAnnotation cmannot = sequence.addContactList(matrix);
pdbAlignment.addAnnotation(cmannot);
return true;
}
git://source.jalview.org / jalview.git / commitdiff