JAL-3851 merged to develop 2022-03-22

[jalview.git] / src / jalview / rest / SelectSequencesEndpoint.java

diff --git a/src/jalview/rest/SelectSequencesEndpoint.java b/src/jalview/rest/SelectSequencesEndpoint.java
new file mode 100644 (file)
index 0000000..7ca5d23
--- /dev/null
+++ b/src/jalview/rest/SelectSequencesEndpoint.java
@@ -0,0 +1,103 @@
+package jalview.rest;
+
+import java.util.Arrays;
+import java.util.List;
+
+import javax.servlet.http.HttpServletRequest;
+import javax.servlet.http.HttpServletResponse;
+
+import jalview.api.AlignViewportI;
+import jalview.api.AlignmentViewPanel;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.SequenceGroup;
+import jalview.datamodel.SequenceI;
+import jalview.gui.AlignFrame;
+
+public class SelectSequencesEndpoint extends AbstractEndpoint
+{
+  public SelectSequencesEndpoint(API api)
+  {
+    super(api, path, name, parameters, description);
+  }
+
+  protected static final String path = "selectsequences";
+
+  private static final String name = "Select sequence(s) positions";
+
+  private static final String parameters = "<sequence names>/<range>";
+
+  private static final String description = "Select the specified sequence(s) with the specified range";
+
+  public void processEndpoint(HttpServletRequest request,
+          HttpServletResponse response)
+  {
+    if (!checkParameters(request, response, 2))
+    {
+      return;
+    }
+    String[] parameters = getEndpointPathParameters(request);
+
+    String rangesString = parameters[1];
+    int[][] ranges = parseIntRanges(rangesString);
+    if (ranges == null || ranges.length < 2 || ranges[0].length < 1)
+    {
+      returnError(request, response,
+              "couldn't parse range '" + rangesString + "'");
+      return;
+    }
+    if (ranges[0].length > 1)
+    {
+      returnError(request, response,
+              "only provide 1 range '" + rangesString + "'");
+      return;
+    }
+    int start = ranges[0][0];
+    int end = ranges[1][0];
+
+    String sequenceNamesString = parameters[0];
+    List<String> sequenceNames = Arrays
+            .asList(sequenceNamesString.split(","));
+
+    AlignFrame[] alignFrames = getAlignFrames(request, true);
+    if (alignFrames == null)
+    {
+      returnError(request, response, "could not find results");
+      return;
+    }
+    for (int i = 0; i < alignFrames.length; i++)
+    {
+      AlignFrame af = alignFrames[i];
+      List<AlignmentViewPanel> aps = (List<AlignmentViewPanel>) af
+              .getAlignPanels();
+      for (AlignmentViewPanel ap : aps)
+      {
+        AlignViewportI avp = ap.getAlignViewport();
+        AlignmentI al = ap.getAlignment();
+        List<SequenceI> seqs = (List<SequenceI>) al.getSequences();
+        SequenceGroup stretchGroup = new SequenceGroup();
+        for (SequenceI seq : seqs)
+        {
+          if (sequenceNames.contains(seq.getName())
+                  || (sequenceNamesString.equals("*")
+                          && alignFrames.length == 1))
+          {
+            stretchGroup.addSequence(seq, false);
+          }
+        }
+        if (start == -1 && end == -1) // "*" as range
+        {
+          stretchGroup.setStartRes(al.getStartRes());
+          stretchGroup.setEndRes(al.getEndRes());
+        }
+        else
+        {
+          stretchGroup.setStartRes(start);
+          stretchGroup.setEndRes(end);
+        }
+        avp.setSelectionGroup(stretchGroup);
+        ap.paintAlignment(false, false);
+        avp.sendSelection();
+      }
+    }
+  }
+}
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