From e95ce7b42f95c193fc6ef5b6efb803d13dbac8b9 Mon Sep 17 00:00:00 2001 From: tcofoegbu Date: Tue, 28 Feb 2017 12:49:20 +0000 Subject: [PATCH] JAL-2136 added improvement to parse crudelist file instead of scrapping 'summary.html' and renamed testfiles accordingly --- .../{c1krhA_.fasta => c1krhA_.1.fasta} | 0 .../{c1krhA_.pdb => c1krhA_.1.pdb} | 0 .../{c1krhA_.scop => c1krhA_.16.scop} | 0 .../{c2piaA_.fasta => c2piaA_.20.fasta} | 0 .../{c2piaA_.pdb => c2piaA_.20.pdb} | 0 .../{c2piaA_.scop => c2piaA_.20.scop} | 0 .../{c4itkA_.fasta => c4itkA_.15.fasta} | 0 .../{c4itkA_.pdb => c4itkA_.15.pdb} | 0 .../{c4itkA_.scop => c4itkA_.15.scop} | 0 .../{c4n58A_.fasta => c4n58A_.1.fasta} | 0 .../{c4n58A_.pdb => c4n58A_.1.pdb} | 0 .../{c4n58A_.scop => c4n58A_.1.scop} | 0 .../{c4wqmA_.fasta => c4wqmA_.19.fasta} | 0 .../{c4wqmA_.pdb => c4wqmA_.19.pdb} | 0 .../{c4wqmA_.scop => c4wqmA_.19.scop} | 0 .../{d1a70a_.fasta => d1a70a_.2.fasta} | 0 .../{d1a70a_.pdb => d1a70a_.2.pdb} | 0 .../{d1a70a_.scop => d1a70a_.2.scop} | 0 .../{d1awda_.fasta => d1awda_.10.fasta} | 0 .../{d1awda_.pdb => d1awda_.10.pdb} | 0 .../{d1awda_.scop => d1awda_.10.scop} | 0 .../{d1czpa_.fasta => d1czpa_.12.fasta} | 0 .../{d1czpa_.pdb => d1czpa_.12.pdb} | 0 .../{d1czpa_.scop => d1czpa_.12.scop} | 0 .../{d1frda_.fasta => d1frda_.6.fasta} | 0 .../{d1frda_.pdb => d1frda_.6.pdb} | 0 .../{d1frda_.scop => d1frda_.6.scop} | 0 .../{d1frra_.fasta => d1frra_.4.fasta} | 0 .../{d1frra_.pdb => d1frra_.4.pdb} | 0 .../{d1frra_.scop => d1frra_.4.scop} | 0 .../{d1fxia_.fasta => d1fxia_.7.fasta} | 0 .../{d1fxia_.pdb => d1fxia_.7.pdb} | 0 .../{d1fxia_.scop => d1fxia_.7.scop} | 0 .../{d1gaqb_.fasta => d1gaqb_.8.fasta} | 0 .../{d1gaqb_.pdb => d1gaqb_.8.pdb} | 0 .../{d1gaqb_.scop => d1gaqb_.8.scop} | 0 .../{d1iuea_.fasta => d1iuea_.9.fasta} | 0 .../{d1iuea_.pdb => d1iuea_.9.pdb} | 0 .../{d1iuea_.scop => d1iuea_.9.scop} | 0 .../{d1jq4a_.fasta => d1jq4a_.18.fasta} | 0 .../{d1jq4a_.pdb => d1jq4a_.18.pdb} | 0 .../{d1jq4a_.scop => d1jq4a_.18.scop} | 0 .../{d1krha3.fasta => d1krha3.17.fasta} | 0 .../{d1krha3.pdb => d1krha3.17.pdb} | 0 .../{d1krha3.scop => d1krha3.17.scop} | 0 .../{d1offa_.fasta => d1offa_.3.fasta} | 0 .../{d1offa_.pdb => d1offa_.3.pdb} | 0 .../{d1offa_.scop => d1offa_.3.scop} | 0 .../{d1pfda_.fasta => d1pfda_.5.fasta} | 0 .../{d1pfda_.pdb => d1pfda_.5.pdb} | 0 .../{d1pfda_.scop => d1pfda_.5.scop} | 0 .../{d1wria_.fasta => d1wria_.11.fasta} | 0 .../{d1wria_.pdb => d1wria_.11.pdb} | 0 .../{d1wria_.scop => d1wria_.11.scop} | 0 .../{d2cjoa_.fasta => d2cjoa_.13.fasta} | 0 .../{d2cjoa_.pdb => d2cjoa_.13.pdb} | 0 .../{d2cjoa_.scop => d2cjoa_.13.scop} | 0 .../{d4fxca_.fasta => d4fxca_.14.fasta} | 0 .../{d4fxca_.pdb => d4fxca_.14.pdb} | 0 .../{d4fxca_.scop => d4fxca_.14.scop} | 0 src/jalview/gui/AppJmol.java | 3 +- src/jalview/gui/StructureChooser.java | 16 ++-- src/jalview/jbgui/GStructureChooser.java | 8 +- src/jalview/ws/phyre2/Phyre2Client.java | 84 +++++--------------- test/jalview/ws/phyre2/Phyre2ClientTest.java | 7 +- 65 files changed, 33 insertions(+), 85 deletions(-) rename examples/testdata/phyre2results/56da5616b4559c93/{c1krhA_.fasta => c1krhA_.1.fasta} (100%) rename examples/testdata/phyre2results/56da5616b4559c93/{c1krhA_.pdb => c1krhA_.1.pdb} (100%) rename examples/testdata/phyre2results/56da5616b4559c93/{c1krhA_.scop => c1krhA_.16.scop} (100%) rename examples/testdata/phyre2results/56da5616b4559c93/{c2piaA_.fasta => c2piaA_.20.fasta} (100%) rename examples/testdata/phyre2results/56da5616b4559c93/{c2piaA_.pdb => c2piaA_.20.pdb} (100%) rename examples/testdata/phyre2results/56da5616b4559c93/{c2piaA_.scop => c2piaA_.20.scop} (100%) rename examples/testdata/phyre2results/56da5616b4559c93/{c4itkA_.fasta => c4itkA_.15.fasta} (100%) rename examples/testdata/phyre2results/56da5616b4559c93/{c4itkA_.pdb => c4itkA_.15.pdb} (100%) rename examples/testdata/phyre2results/56da5616b4559c93/{c4itkA_.scop => c4itkA_.15.scop} (100%) rename examples/testdata/phyre2results/56da5616b4559c93/{c4n58A_.fasta => c4n58A_.1.fasta} (100%) rename examples/testdata/phyre2results/56da5616b4559c93/{c4n58A_.pdb => c4n58A_.1.pdb} (100%) rename examples/testdata/phyre2results/56da5616b4559c93/{c4n58A_.scop => c4n58A_.1.scop} (100%) rename examples/testdata/phyre2results/56da5616b4559c93/{c4wqmA_.fasta => c4wqmA_.19.fasta} (100%) rename examples/testdata/phyre2results/56da5616b4559c93/{c4wqmA_.pdb => c4wqmA_.19.pdb} (100%) rename examples/testdata/phyre2results/56da5616b4559c93/{c4wqmA_.scop => c4wqmA_.19.scop} (100%) rename examples/testdata/phyre2results/56da5616b4559c93/{d1a70a_.fasta => d1a70a_.2.fasta} (100%) rename examples/testdata/phyre2results/56da5616b4559c93/{d1a70a_.pdb => d1a70a_.2.pdb} (100%) rename examples/testdata/phyre2results/56da5616b4559c93/{d1a70a_.scop => d1a70a_.2.scop} (100%) rename examples/testdata/phyre2results/56da5616b4559c93/{d1awda_.fasta => d1awda_.10.fasta} (100%) rename examples/testdata/phyre2results/56da5616b4559c93/{d1awda_.pdb => d1awda_.10.pdb} (100%) rename examples/testdata/phyre2results/56da5616b4559c93/{d1awda_.scop => d1awda_.10.scop} (100%) rename examples/testdata/phyre2results/56da5616b4559c93/{d1czpa_.fasta => d1czpa_.12.fasta} (100%) rename examples/testdata/phyre2results/56da5616b4559c93/{d1czpa_.pdb => d1czpa_.12.pdb} (100%) rename examples/testdata/phyre2results/56da5616b4559c93/{d1czpa_.scop => d1czpa_.12.scop} (100%) rename examples/testdata/phyre2results/56da5616b4559c93/{d1frda_.fasta => d1frda_.6.fasta} (100%) rename examples/testdata/phyre2results/56da5616b4559c93/{d1frda_.pdb => d1frda_.6.pdb} (100%) rename examples/testdata/phyre2results/56da5616b4559c93/{d1frda_.scop => d1frda_.6.scop} (100%) rename examples/testdata/phyre2results/56da5616b4559c93/{d1frra_.fasta => d1frra_.4.fasta} (100%) rename examples/testdata/phyre2results/56da5616b4559c93/{d1frra_.pdb => d1frra_.4.pdb} (100%) rename examples/testdata/phyre2results/56da5616b4559c93/{d1frra_.scop => d1frra_.4.scop} (100%) rename examples/testdata/phyre2results/56da5616b4559c93/{d1fxia_.fasta => d1fxia_.7.fasta} (100%) rename examples/testdata/phyre2results/56da5616b4559c93/{d1fxia_.pdb => d1fxia_.7.pdb} (100%) rename examples/testdata/phyre2results/56da5616b4559c93/{d1fxia_.scop => d1fxia_.7.scop} (100%) rename examples/testdata/phyre2results/56da5616b4559c93/{d1gaqb_.fasta => d1gaqb_.8.fasta} (100%) rename examples/testdata/phyre2results/56da5616b4559c93/{d1gaqb_.pdb => d1gaqb_.8.pdb} (100%) rename examples/testdata/phyre2results/56da5616b4559c93/{d1gaqb_.scop => d1gaqb_.8.scop} (100%) rename examples/testdata/phyre2results/56da5616b4559c93/{d1iuea_.fasta => d1iuea_.9.fasta} (100%) rename examples/testdata/phyre2results/56da5616b4559c93/{d1iuea_.pdb => d1iuea_.9.pdb} (100%) rename examples/testdata/phyre2results/56da5616b4559c93/{d1iuea_.scop => d1iuea_.9.scop} (100%) rename examples/testdata/phyre2results/56da5616b4559c93/{d1jq4a_.fasta => d1jq4a_.18.fasta} (100%) rename examples/testdata/phyre2results/56da5616b4559c93/{d1jq4a_.pdb => d1jq4a_.18.pdb} (100%) rename examples/testdata/phyre2results/56da5616b4559c93/{d1jq4a_.scop => d1jq4a_.18.scop} (100%) rename examples/testdata/phyre2results/56da5616b4559c93/{d1krha3.fasta => d1krha3.17.fasta} (100%) rename examples/testdata/phyre2results/56da5616b4559c93/{d1krha3.pdb => d1krha3.17.pdb} (100%) rename examples/testdata/phyre2results/56da5616b4559c93/{d1krha3.scop => d1krha3.17.scop} (100%) rename examples/testdata/phyre2results/56da5616b4559c93/{d1offa_.fasta => d1offa_.3.fasta} (100%) rename examples/testdata/phyre2results/56da5616b4559c93/{d1offa_.pdb => d1offa_.3.pdb} (100%) rename examples/testdata/phyre2results/56da5616b4559c93/{d1offa_.scop => d1offa_.3.scop} (100%) rename examples/testdata/phyre2results/56da5616b4559c93/{d1pfda_.fasta => d1pfda_.5.fasta} (100%) rename examples/testdata/phyre2results/56da5616b4559c93/{d1pfda_.pdb => d1pfda_.5.pdb} (100%) rename examples/testdata/phyre2results/56da5616b4559c93/{d1pfda_.scop => d1pfda_.5.scop} (100%) rename examples/testdata/phyre2results/56da5616b4559c93/{d1wria_.fasta => d1wria_.11.fasta} (100%) rename examples/testdata/phyre2results/56da5616b4559c93/{d1wria_.pdb => d1wria_.11.pdb} (100%) rename examples/testdata/phyre2results/56da5616b4559c93/{d1wria_.scop => d1wria_.11.scop} (100%) rename examples/testdata/phyre2results/56da5616b4559c93/{d2cjoa_.fasta => d2cjoa_.13.fasta} (100%) rename examples/testdata/phyre2results/56da5616b4559c93/{d2cjoa_.pdb => d2cjoa_.13.pdb} (100%) rename examples/testdata/phyre2results/56da5616b4559c93/{d2cjoa_.scop => d2cjoa_.13.scop} (100%) rename examples/testdata/phyre2results/56da5616b4559c93/{d4fxca_.fasta => d4fxca_.14.fasta} (100%) rename examples/testdata/phyre2results/56da5616b4559c93/{d4fxca_.pdb => d4fxca_.14.pdb} (100%) rename examples/testdata/phyre2results/56da5616b4559c93/{d4fxca_.scop => d4fxca_.14.scop} (100%) diff --git a/examples/testdata/phyre2results/56da5616b4559c93/c1krhA_.fasta b/examples/testdata/phyre2results/56da5616b4559c93/c1krhA_.1.fasta similarity index 100% rename from examples/testdata/phyre2results/56da5616b4559c93/c1krhA_.fasta rename to examples/testdata/phyre2results/56da5616b4559c93/c1krhA_.1.fasta diff --git a/examples/testdata/phyre2results/56da5616b4559c93/c1krhA_.pdb b/examples/testdata/phyre2results/56da5616b4559c93/c1krhA_.1.pdb similarity index 100% rename from examples/testdata/phyre2results/56da5616b4559c93/c1krhA_.pdb rename to examples/testdata/phyre2results/56da5616b4559c93/c1krhA_.1.pdb diff --git a/examples/testdata/phyre2results/56da5616b4559c93/c1krhA_.scop b/examples/testdata/phyre2results/56da5616b4559c93/c1krhA_.16.scop similarity index 100% rename from examples/testdata/phyre2results/56da5616b4559c93/c1krhA_.scop rename to examples/testdata/phyre2results/56da5616b4559c93/c1krhA_.16.scop diff --git a/examples/testdata/phyre2results/56da5616b4559c93/c2piaA_.fasta b/examples/testdata/phyre2results/56da5616b4559c93/c2piaA_.20.fasta similarity index 100% rename from examples/testdata/phyre2results/56da5616b4559c93/c2piaA_.fasta rename to examples/testdata/phyre2results/56da5616b4559c93/c2piaA_.20.fasta diff --git a/examples/testdata/phyre2results/56da5616b4559c93/c2piaA_.pdb b/examples/testdata/phyre2results/56da5616b4559c93/c2piaA_.20.pdb similarity index 100% rename from examples/testdata/phyre2results/56da5616b4559c93/c2piaA_.pdb rename to examples/testdata/phyre2results/56da5616b4559c93/c2piaA_.20.pdb diff --git a/examples/testdata/phyre2results/56da5616b4559c93/c2piaA_.scop b/examples/testdata/phyre2results/56da5616b4559c93/c2piaA_.20.scop similarity index 100% rename from examples/testdata/phyre2results/56da5616b4559c93/c2piaA_.scop rename to examples/testdata/phyre2results/56da5616b4559c93/c2piaA_.20.scop diff --git a/examples/testdata/phyre2results/56da5616b4559c93/c4itkA_.fasta b/examples/testdata/phyre2results/56da5616b4559c93/c4itkA_.15.fasta similarity index 100% rename from examples/testdata/phyre2results/56da5616b4559c93/c4itkA_.fasta rename to examples/testdata/phyre2results/56da5616b4559c93/c4itkA_.15.fasta diff --git a/examples/testdata/phyre2results/56da5616b4559c93/c4itkA_.pdb b/examples/testdata/phyre2results/56da5616b4559c93/c4itkA_.15.pdb similarity index 100% rename from examples/testdata/phyre2results/56da5616b4559c93/c4itkA_.pdb rename to examples/testdata/phyre2results/56da5616b4559c93/c4itkA_.15.pdb diff --git a/examples/testdata/phyre2results/56da5616b4559c93/c4itkA_.scop b/examples/testdata/phyre2results/56da5616b4559c93/c4itkA_.15.scop similarity index 100% rename from examples/testdata/phyre2results/56da5616b4559c93/c4itkA_.scop rename to examples/testdata/phyre2results/56da5616b4559c93/c4itkA_.15.scop diff --git a/examples/testdata/phyre2results/56da5616b4559c93/c4n58A_.fasta b/examples/testdata/phyre2results/56da5616b4559c93/c4n58A_.1.fasta similarity index 100% rename from examples/testdata/phyre2results/56da5616b4559c93/c4n58A_.fasta rename to examples/testdata/phyre2results/56da5616b4559c93/c4n58A_.1.fasta diff --git a/examples/testdata/phyre2results/56da5616b4559c93/c4n58A_.pdb b/examples/testdata/phyre2results/56da5616b4559c93/c4n58A_.1.pdb similarity index 100% rename from examples/testdata/phyre2results/56da5616b4559c93/c4n58A_.pdb rename to examples/testdata/phyre2results/56da5616b4559c93/c4n58A_.1.pdb diff --git a/examples/testdata/phyre2results/56da5616b4559c93/c4n58A_.scop b/examples/testdata/phyre2results/56da5616b4559c93/c4n58A_.1.scop similarity index 100% rename from examples/testdata/phyre2results/56da5616b4559c93/c4n58A_.scop rename to examples/testdata/phyre2results/56da5616b4559c93/c4n58A_.1.scop diff --git a/examples/testdata/phyre2results/56da5616b4559c93/c4wqmA_.fasta b/examples/testdata/phyre2results/56da5616b4559c93/c4wqmA_.19.fasta similarity index 100% rename from examples/testdata/phyre2results/56da5616b4559c93/c4wqmA_.fasta rename to examples/testdata/phyre2results/56da5616b4559c93/c4wqmA_.19.fasta diff --git a/examples/testdata/phyre2results/56da5616b4559c93/c4wqmA_.pdb b/examples/testdata/phyre2results/56da5616b4559c93/c4wqmA_.19.pdb similarity index 100% rename from examples/testdata/phyre2results/56da5616b4559c93/c4wqmA_.pdb rename to examples/testdata/phyre2results/56da5616b4559c93/c4wqmA_.19.pdb diff --git a/examples/testdata/phyre2results/56da5616b4559c93/c4wqmA_.scop b/examples/testdata/phyre2results/56da5616b4559c93/c4wqmA_.19.scop similarity index 100% rename from examples/testdata/phyre2results/56da5616b4559c93/c4wqmA_.scop rename to examples/testdata/phyre2results/56da5616b4559c93/c4wqmA_.19.scop diff --git a/examples/testdata/phyre2results/56da5616b4559c93/d1a70a_.fasta b/examples/testdata/phyre2results/56da5616b4559c93/d1a70a_.2.fasta similarity index 100% rename from examples/testdata/phyre2results/56da5616b4559c93/d1a70a_.fasta rename to examples/testdata/phyre2results/56da5616b4559c93/d1a70a_.2.fasta diff --git a/examples/testdata/phyre2results/56da5616b4559c93/d1a70a_.pdb b/examples/testdata/phyre2results/56da5616b4559c93/d1a70a_.2.pdb similarity index 100% rename from examples/testdata/phyre2results/56da5616b4559c93/d1a70a_.pdb rename to examples/testdata/phyre2results/56da5616b4559c93/d1a70a_.2.pdb diff --git a/examples/testdata/phyre2results/56da5616b4559c93/d1a70a_.scop b/examples/testdata/phyre2results/56da5616b4559c93/d1a70a_.2.scop similarity index 100% rename from examples/testdata/phyre2results/56da5616b4559c93/d1a70a_.scop rename to examples/testdata/phyre2results/56da5616b4559c93/d1a70a_.2.scop diff --git a/examples/testdata/phyre2results/56da5616b4559c93/d1awda_.fasta b/examples/testdata/phyre2results/56da5616b4559c93/d1awda_.10.fasta similarity index 100% rename from examples/testdata/phyre2results/56da5616b4559c93/d1awda_.fasta rename to examples/testdata/phyre2results/56da5616b4559c93/d1awda_.10.fasta diff --git a/examples/testdata/phyre2results/56da5616b4559c93/d1awda_.pdb b/examples/testdata/phyre2results/56da5616b4559c93/d1awda_.10.pdb similarity index 100% rename from examples/testdata/phyre2results/56da5616b4559c93/d1awda_.pdb rename to examples/testdata/phyre2results/56da5616b4559c93/d1awda_.10.pdb diff --git a/examples/testdata/phyre2results/56da5616b4559c93/d1awda_.scop b/examples/testdata/phyre2results/56da5616b4559c93/d1awda_.10.scop similarity index 100% rename from examples/testdata/phyre2results/56da5616b4559c93/d1awda_.scop rename to examples/testdata/phyre2results/56da5616b4559c93/d1awda_.10.scop diff --git a/examples/testdata/phyre2results/56da5616b4559c93/d1czpa_.fasta 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examples/testdata/phyre2results/56da5616b4559c93/d4fxca_.14.pdb diff --git a/examples/testdata/phyre2results/56da5616b4559c93/d4fxca_.scop b/examples/testdata/phyre2results/56da5616b4559c93/d4fxca_.14.scop similarity index 100% rename from examples/testdata/phyre2results/56da5616b4559c93/d4fxca_.scop rename to examples/testdata/phyre2results/56da5616b4559c93/d4fxca_.14.scop diff --git a/src/jalview/gui/AppJmol.java b/src/jalview/gui/AppJmol.java index 5f18aea..bdd8c4b 100644 --- a/src/jalview/gui/AppJmol.java +++ b/src/jalview/gui/AppJmol.java @@ -66,7 +66,6 @@ import javax.swing.JCheckBoxMenuItem; import javax.swing.JColorChooser; import javax.swing.JInternalFrame; import javax.swing.JMenu; -import javax.swing.JOptionPane; import javax.swing.JPanel; import javax.swing.JSplitPane; import javax.swing.SwingUtilities; @@ -164,7 +163,7 @@ public class AppJmol extends StructureViewerBase closeViewer(false); } }); - initJmol(loadStatus); // pdbentry, seq, JBPCHECK! + initJmol(loadStatus); // pdbentry, seq, JBPCHECK!ˇ } diff --git a/src/jalview/gui/StructureChooser.java b/src/jalview/gui/StructureChooser.java index bff6d6f..cad168f 100644 --- 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 phyreResults = Phyre2Client + // .parsePhyre2ResultSummaryTable(summaryhtml); + + String crudeListFile = phyre2ResultDirectory + "crudelist"; List phyreResults = Phyre2Client - .parsePhyre2ResultSummaryTable(summaryhtml); + .parsePhyreCrudeList(crudeListFile); + getPhyreResultTable() .setModel(Phyre2Client.getTableModel(phyreResults)); Phyre2Client.configurePhyreResultTable(getPhyreResultTable()); diff --git a/src/jalview/jbgui/GStructureChooser.java b/src/jalview/jbgui/GStructureChooser.java index 5a185f8..e4e73d1 100644 --- a/src/jalview/jbgui/GStructureChooser.java +++ b/src/jalview/jbgui/GStructureChooser.java @@ -654,13 +654,9 @@ public abstract class GStructureChooser extends JPanel implements protected void closeAction(int preferredHeight) { - // System.out.println(">>>>>>>>>> closing internal frame!!!"); - // System.out.println("width : " + mainFrame.getWidth()); - // System.out.println("heigh : " + mainFrame.getHeight()); - // System.out.println("x : " + mainFrame.getX()); - // System.out.println("y : " + mainFrame.getY()); tempUserPrefs.put("structureChooser.width", pnl_filter.getWidth()); - tempUserPrefs.put("structureChooser.height", preferredHeight); + tempUserPrefs.put("structureChooser.height", + pnl_filter.getHeight() - 76); tempUserPrefs.put("structureChooser.x", mainFrame.getX()); tempUserPrefs.put("structureChooser.y", mainFrame.getY()); mainFrame.dispose(); diff --git a/src/jalview/ws/phyre2/Phyre2Client.java b/src/jalview/ws/phyre2/Phyre2Client.java index 0a29412..e980a19 100644 --- a/src/jalview/ws/phyre2/Phyre2Client.java +++ b/src/jalview/ws/phyre2/Phyre2Client.java @@ -14,7 +14,9 @@ import jalview.structures.models.MappingOutputModel; import jalview.util.Comparison; import jalview.util.Format; +import java.io.BufferedReader; import java.io.File; +import java.io.FileReader; import java.io.IOException; import java.io.PrintStream; import java.util.ArrayList; @@ -24,11 +26,6 @@ import java.util.List; import javax.swing.JTable; import javax.swing.table.DefaultTableModel; -import org.jsoup.Jsoup; -import org.jsoup.nodes.Document; -import org.jsoup.nodes.Element; -import org.jsoup.select.Elements; - public class Phyre2Client extends StructureMappingClient { private final static String NEWLINE = System.lineSeparator(); @@ -293,73 +290,30 @@ public class Phyre2Client extends StructureMappingClient } - - public static List parsePhyre2ResultSummaryTable( - String html) + public static List parsePhyreCrudeList(String crudeList) { List phyre2Results = new ArrayList(); - try + try (BufferedReader br = new BufferedReader(new FileReader(crudeList))) { - File in = new File(html); - Document doc = Jsoup.parse(in, null); - // Document doc = Jsoup.connect(html).get(); - Elements tableElements = doc.select("table.midshade"); - for (Element table : tableElements) + String line; + while ((line = br.readLine()) != null) { - System.out.println(); - Elements tableRowElements = table.select(":not(thead) tr"); - for (int i = 0; i < tableRowElements.size(); i++) - { - Element row = tableRowElements.get(i); - Elements rowItems = row.select("td"); - if (rowItems.size() > 11) - { - // for (int j = 0; j < rowItems.size(); j++) - // { - // System.out.println(">>> r:" + j + " = " - // + rowItems.get(j).text()); - // } - - String c = rowItems.get(6).select("input").attr("onmouseover"); - String alignedRange = c.substring(c.indexOf("Residues ") + 9, - c.indexOf(" of your sequence aligned ")); - String coverage = c.substring(c.lastIndexOf(" (") + 2, - c.lastIndexOf(" coverage). Click to view detailed")); - // System.out.println("coverage" + coverage); - try - { - Phyre2SummaryPojo psp = new Phyre2SummaryPojo(); - String sn = rowItems.get(0).text(); - psp.setSerialNo(Integer.valueOf(sn)); - psp.setTemplateId(rowItems.get(1).text()); - psp.setCoverage(coverage); - psp.setAlignedRange(alignedRange); - psp.setConfidence(Double.valueOf(rowItems.get(8).text())); - psp.setPid(Integer.valueOf(rowItems.get(9).text())); - psp.setTemplateSummary(rowItems.get(10).text()); - // System.out.println("row >>>> " + psp.toString()); - // System.out.println(); - phyre2Results.add(psp); - } catch (NumberFormatException e) - { - e.printStackTrace(); - } catch (IndexOutOfBoundsException e) - { - e.printStackTrace(); - } catch (Exception e) - { - e.printStackTrace(); - } - } - } + String[] lineData = line.split(" "); + Phyre2SummaryPojo psp = new Phyre2SummaryPojo(); + psp.setSerialNo(Integer.valueOf(lineData[0])); + psp.setTemplateId(lineData[1]); + psp.setConfidence(100 * Double.valueOf(lineData[2])); + psp.setPid(Integer.valueOf(lineData[3])); + psp.setAlignedRange(lineData[4] + " - " + lineData[5]); + // psp.setCoverage(coverage); + // psp.setTemplateSummary(templateSummary); + phyre2Results.add(psp); } - return phyre2Results; - } catch (Exception e) { e.printStackTrace(); - return null; } + return phyre2Results; } public static DefaultTableModel getTableModel( @@ -436,8 +390,8 @@ public class Phyre2Client extends StructureMappingClient phyreResultTable.getColumn("#").setCellRenderer(idCellRender); phyreResultTable.getColumn("Template").setMinWidth(60); - phyreResultTable.getColumn("Template").setPreferredWidth(60); - phyreResultTable.getColumn("Template").setMaxWidth(90); + phyreResultTable.getColumn("Template").setPreferredWidth(90); + phyreResultTable.getColumn("Template").setMaxWidth(150); phyreResultTable.getColumn("Aligned Range").setMinWidth(80); phyreResultTable.getColumn("Aligned Range").setPreferredWidth(80); diff --git a/test/jalview/ws/phyre2/Phyre2ClientTest.java b/test/jalview/ws/phyre2/Phyre2ClientTest.java index 322bfa3..811ddd0 100644 --- a/test/jalview/ws/phyre2/Phyre2ClientTest.java +++ b/test/jalview/ws/phyre2/Phyre2ClientTest.java @@ -393,10 +393,5 @@ public class Phyre2ClientTest } } - @Test(groups = { "Functional" }) - public void readPhyre2SummaryTableTest() - { - String summaryhtml = "examples/testdata/phyre2results/56da5616b4559c93/summary.html"; - Phyre2Client.parsePhyre2ResultSummaryTable(summaryhtml); - } + } -- 1.7.10.2