JAL-2136 added improvement to parse crudelist file instead of scrapping 'summary...

[jalview.git] / src / jalview / gui / StructureChooser.java

diff --git a/src/jalview/gui/StructureChooser.java b/src/jalview/gui/StructureChooser.java
index bff6d6f..cad168f 100644 (file)
--- a/src/jalview/gui/StructureChooser.java
+++ b/src/jalview/gui/StructureChooser.java
@@ -908,8 +908,7 @@ public class StructureChooser extends GStructureChooser implements
           {
             String templateId = getPhyreResultTable().getValueAt(row,
                     templateColIndex).toString();
-            String structureFile = phyre2ResultDirectory + templateId
-                    + ".pdb";
+            String structureFile = phyre2ResultDirectory + templateId;
             pdbEntriesToView[count++] = new AssociateStructureFileWithSeq()
                     .associateStructureWithSeq(structureFile,
                             DataSourceType.FILE, selectedSequence, true,
@@ -964,11 +963,16 @@ public class StructureChooser extends GStructureChooser implements
     // for getting the result directory when the job completes, this is
     // currently hard-wired to the directory of result for FER_CAPAN/1-144
     phyre2ResultDirectory = "examples/testdata/phyre2results/56da5616b4559c93/";
-    String summaryhtml = phyre2ResultDirectory + "summary.html";
-    // TODO ditch HTML parsing once appropriated data file (i.e. JSON) for
-    // Phyre2 result summary is made available
+    // String summaryhtml = phyre2ResultDirectory + "summary.html";
+    // // TODO ditch HTML parsing once appropriated data file (i.e. JSON) for
+    // // Phyre2 result summary is made available
+    // List<Phyre2SummaryPojo> phyreResults = Phyre2Client
+    // .parsePhyre2ResultSummaryTable(summaryhtml);
+
+    String crudeListFile = phyre2ResultDirectory + "crudelist";
     List<Phyre2SummaryPojo> phyreResults = Phyre2Client
-            .parsePhyre2ResultSummaryTable(summaryhtml);
+            .parsePhyreCrudeList(crudeListFile);
+
     getPhyreResultTable()
             .setModel(Phyre2Client.getTableModel(phyreResults));
     Phyre2Client.configurePhyreResultTable(getPhyreResultTable());