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JAL-1821 updated the reference sequence column of structure chooser summary table...
author
tcofoegbu
<tcnofoegbu@dundee.ac.uk>
Tue, 4 Aug 2015 09:49:26 +0000
(10:49 +0100)
committer
tcofoegbu
<tcnofoegbu@dundee.ac.uk>
Tue, 4 Aug 2015 09:49:26 +0000
(10:49 +0100)
src/jalview/datamodel/Sequence.java
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src/jalview/gui/PDBSearchPanel.java
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src/jalview/gui/StructureChooser.java
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src/jalview/jbgui/GStructureChooser.java
patch
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src/jalview/ws/dbsources/PDBRestClient.java
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src/jalview/ws/uimodel/PDBRestRequest.java
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src/jalview/ws/uimodel/PDBRestResponse.java
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diff --git
a/src/jalview/datamodel/Sequence.java
b/src/jalview/datamodel/Sequence.java
index
c78ec22
..
916d785
100755
(executable)
--- a/
src/jalview/datamodel/Sequence.java
+++ b/
src/jalview/datamodel/Sequence.java
@@
-1302,5
+1302,9
@@
public class Sequence extends ASequence implements SequenceI
return result;
}
return result;
}
+ public String toString()
+ {
+ return getDisplayId(false);
+ }
}
}
diff --git
a/src/jalview/gui/PDBSearchPanel.java
b/src/jalview/gui/PDBSearchPanel.java
index
964a7d8
..
06aa5df
100644
(file)
--- a/
src/jalview/gui/PDBSearchPanel.java
+++ b/
src/jalview/gui/PDBSearchPanel.java
@@
-98,6
+98,7
@@
public class PDBSearchPanel extends GPDBSearchPanel
// System.out.println(">>>>>>>>>>>>>>>" + e.getMessage());
// JOptionPane.showMessageDialog(this, e.getMessage(),
// "PDB Web-service Error", JOptionPane.ERROR_MESSAGE);
// System.out.println(">>>>>>>>>>>>>>>" + e.getMessage());
// JOptionPane.showMessageDialog(this, e.getMessage(),
// "PDB Web-service Error", JOptionPane.ERROR_MESSAGE);
+ e.printStackTrace();
errorWarning.append(e.getMessage());
checkForErrors();
return;
errorWarning.append(e.getMessage());
checkForErrors();
return;
diff --git
a/src/jalview/gui/StructureChooser.java
b/src/jalview/gui/StructureChooser.java
index
3540cfc
..
3db26f3
100644
(file)
--- a/
src/jalview/gui/StructureChooser.java
+++ b/
src/jalview/gui/StructureChooser.java
@@
-153,7
+153,7
@@
public class StructureChooser extends GStructureChooser
pdbRequest.setFieldToSearchBy("(text:");
pdbRequest.setWantedFields(wantedFields);
pdbRequest.setSearchTerm(buildQuery(seq) + ")");
pdbRequest.setFieldToSearchBy("(text:");
pdbRequest.setWantedFields(wantedFields);
pdbRequest.setSearchTerm(buildQuery(seq) + ")");
- pdbRequest.setAssociatedSequence(seq.getName());
+ pdbRequest.setAssociatedSequence(seq);
pdbRestCleint = new PDBRestClient();
PDBRestResponse resultList;
try
pdbRestCleint = new PDBRestClient();
PDBRestResponse resultList;
try
@@
-161,6
+161,7
@@
public class StructureChooser extends GStructureChooser
resultList = pdbRestCleint.executeRequest(pdbRequest);
} catch (Exception e)
{
resultList = pdbRestCleint.executeRequest(pdbRequest);
} catch (Exception e)
{
+ e.printStackTrace();
errors.add(e.getMessage());
continue;
}
errors.add(e.getMessage());
continue;
}
@@
-336,7
+337,7
@@
public class StructureChooser extends GStructureChooser
*/
public static boolean isValidSeqName(String seqName)
{
*/
public static boolean isValidSeqName(String seqName)
{
- System.out.println("seqName : " + seqName);
+ // System.out.println("seqName : " + seqName);
String ignoreList = "pdb,uniprot,swiss-prot";
if (seqName.length() < 3)
{
String ignoreList = "pdb,uniprot,swiss-prot";
if (seqName.length() < 3)
{
@@
-392,7
+393,7
@@
public class StructureChooser extends GStructureChooser
!chk_invertFilter.isSelected());
pdbRequest.setSearchTerm(buildQuery(seq) + ")");
pdbRequest.setWantedFields(wantedFields);
!chk_invertFilter.isSelected());
pdbRequest.setSearchTerm(buildQuery(seq) + ")");
pdbRequest.setWantedFields(wantedFields);
- pdbRequest.setAssociatedSequence(seq.getName());
+ pdbRequest.setAssociatedSequence(seq);
pdbRestCleint = new PDBRestClient();
PDBRestResponse resultList;
try
pdbRestCleint = new PDBRestClient();
PDBRestResponse resultList;
try
@@
-400,6
+401,7
@@
public class StructureChooser extends GStructureChooser
resultList = pdbRestCleint.executeRequest(pdbRequest);
} catch (Exception e)
{
resultList = pdbRestCleint.executeRequest(pdbRequest);
} catch (Exception e)
{
+ e.printStackTrace();
errors.add(e.getMessage());
continue;
}
errors.add(e.getMessage());
continue;
}
@@
-675,16
+677,21
@@
public class StructureChooser extends GStructureChooser
String currentView = selectedFilterOpt.getView();
if (currentView == VIEWS_FILTER)
{
String currentView = selectedFilterOpt.getView();
if (currentView == VIEWS_FILTER)
{
- int pdbIdCol = PDBRestClient.getPDBIdColumIndex(
- lastPdbRequest.getWantedFields(), true);
+ int pdbIdColIndex = tbl_summary.getColumn(
+ PDBRestClient.PDBDocField.PDB_ID.getName()).getModelIndex();
+ int refSeqColIndex = tbl_summary.getColumn("Ref Sequence")
+ .getModelIndex();
int[] selectedRows = tbl_summary.getSelectedRows();
PDBEntry[] pdbEntriesToView = new PDBEntry[selectedRows.length];
int count = 0;
int[] selectedRows = tbl_summary.getSelectedRows();
PDBEntry[] pdbEntriesToView = new PDBEntry[selectedRows.length];
int count = 0;
+ ArrayList<SequenceI> selectedSeqsToView = new ArrayList<SequenceI>();
for (int summaryRow : selectedRows)
{
for (int summaryRow : selectedRows)
{
- String pdbIdStr = tbl_summary.getValueAt(summaryRow, pdbIdCol)
+ String pdbIdStr = tbl_summary.getValueAt(summaryRow, pdbIdColIndex)
.toString();
.toString();
-
+ SequenceI selectedSeq = (SequenceI) tbl_summary.getValueAt(
+ summaryRow, refSeqColIndex);
+ selectedSeqsToView.add(selectedSeq);
PDBEntry pdbEntry = cachedEntryMap.get(pdbIdStr.toLowerCase());
if (pdbEntry == null)
{
PDBEntry pdbEntry = cachedEntryMap.get(pdbIdStr.toLowerCase());
if (pdbEntry == null)
{
@@
-694,8
+701,10
@@
public class StructureChooser extends GStructureChooser
}
pdbEntriesToView[count++] = pdbEntry;
}
}
pdbEntriesToView[count++] = pdbEntry;
}
+ SequenceI[] selectedSeqs = selectedSeqsToView
+ .toArray(new SequenceI[selectedSeqsToView.size()]);
launchStructureViewer(ap.getStructureSelectionManager(),
launchStructureViewer(ap.getStructureSelectionManager(),
- pdbEntriesToView, ap, selectedSequences);
+ pdbEntriesToView, ap, selectedSeqs);
}
else if(currentView == VIEWS_LOCAL_PDB){
int[] selectedRows = tbl_local_pdb.getSelectedRows();
}
else if(currentView == VIEWS_LOCAL_PDB){
int[] selectedRows = tbl_local_pdb.getSelectedRows();
@@
-832,7
+841,7
@@
public class StructureChooser extends GStructureChooser
pdbRequest.setFieldToSearchBy("(pdb_id:");
pdbRequest.setWantedFields(wantedFields);
pdbRequest.setSearchTerm(txt_search.getText() + ")");
pdbRequest.setFieldToSearchBy("(pdb_id:");
pdbRequest.setWantedFields(wantedFields);
pdbRequest.setSearchTerm(txt_search.getText() + ")");
- pdbRequest.setAssociatedSequence(selectedSequence.getName());
+ pdbRequest.setAssociatedSequence(selectedSequence);
pdbRestCleint = new PDBRestClient();
PDBRestResponse resultList;
try
pdbRestCleint = new PDBRestClient();
PDBRestResponse resultList;
try
diff --git
a/src/jalview/jbgui/GStructureChooser.java
b/src/jalview/jbgui/GStructureChooser.java
index
d0f2328
..
9c016f9
100644
(file)
--- a/
src/jalview/jbgui/GStructureChooser.java
+++ b/
src/jalview/jbgui/GStructureChooser.java
@@
-181,6
+181,7
@@
public abstract class GStructureChooser extends JPanel implements
private void jbInit() throws Exception
{
tbl_summary.setAutoCreateRowSorter(true);
private void jbInit() throws Exception
{
tbl_summary.setAutoCreateRowSorter(true);
+ tbl_summary.getTableHeader().setReorderingAllowed(false);
tbl_local_pdb.setAutoCreateRowSorter(true);
tbl_local_pdb.addMouseListener(new MouseAdapter()
{
tbl_local_pdb.setAutoCreateRowSorter(true);
tbl_local_pdb.addMouseListener(new MouseAdapter()
{
diff --git
a/src/jalview/ws/dbsources/PDBRestClient.java
b/src/jalview/ws/dbsources/PDBRestClient.java
index
09c10ef
..
7e80126
100644
(file)
--- a/
src/jalview/ws/dbsources/PDBRestClient.java
+++ b/
src/jalview/ws/dbsources/PDBRestClient.java
@@
-59,7
+59,6
@@
public class PDBRestClient
.getFieldToSortBy().trim().isEmpty()) ? "" : (pdbRestRequest
.getFieldToSortBy() + (pdbRestRequest.isAscending() ? " asc"
: " desc"));
.getFieldToSortBy().trim().isEmpty()) ? "" : (pdbRestRequest
.getFieldToSortBy() + (pdbRestRequest.isAscending() ? " asc"
: " desc"));
-
// Build request parameters for the REST Request
WebResource webResource = client.resource(PDB_SEARCH_ENDPOINT)
.queryParam("wt", "json").queryParam("fl", wantedFields)
// Build request parameters for the REST Request
WebResource webResource = client.resource(PDB_SEARCH_ENDPOINT)
.queryParam("wt", "json").queryParam("fl", wantedFields)
diff --git
a/src/jalview/ws/uimodel/PDBRestRequest.java
b/src/jalview/ws/uimodel/PDBRestRequest.java
index
58d7aeb
..
1bf8b35
100644
(file)
--- a/
src/jalview/ws/uimodel/PDBRestRequest.java
+++ b/
src/jalview/ws/uimodel/PDBRestRequest.java
@@
-22,6
+22,7
@@
package jalview.ws.uimodel;
package jalview.ws.uimodel;
+import jalview.datamodel.SequenceI;
import jalview.ws.dbsources.PDBRestClient.PDBDocField;
import java.util.Collection;
import jalview.ws.dbsources.PDBRestClient.PDBDocField;
import java.util.Collection;
@@
-40,7
+41,7
@@
public class PDBRestRequest
private String fieldToSortBy;
private String fieldToSortBy;
- private String associatedSequence;
+ private SequenceI associatedSequence;
private boolean allowEmptySequence;
private boolean allowEmptySequence;
@@
-117,12
+118,12
@@
public class PDBRestRequest
return isSortAscending;
}
return isSortAscending;
}
- public String getAssociatedSequence()
+ public SequenceI getAssociatedSequence()
{
return associatedSequence;
}
{
return associatedSequence;
}
- public void setAssociatedSequence(String associatedSequence)
+ public void setAssociatedSequence(SequenceI associatedSequence)
{
this.associatedSequence = associatedSequence;
}
{
this.associatedSequence = associatedSequence;
}
diff --git
a/src/jalview/ws/uimodel/PDBRestResponse.java
b/src/jalview/ws/uimodel/PDBRestResponse.java
index
0a33672
..
b82b997
100644
(file)
--- a/
src/jalview/ws/uimodel/PDBRestResponse.java
+++ b/
src/jalview/ws/uimodel/PDBRestResponse.java
@@
-21,6
+21,7
@@
package jalview.ws.uimodel;
package jalview.ws.uimodel;
+import jalview.datamodel.SequenceI;
import jalview.ws.dbsources.PDBRestClient.PDBDocField;
import java.util.Collection;
import jalview.ws.dbsources.PDBRestClient.PDBDocField;
import java.util.Collection;
@@
-101,7
+102,7
@@
public class PDBRestResponse
};
if (request.getAssociatedSequence() != null)
{
};
if (request.getAssociatedSequence() != null)
{
- tableModel.addColumn("Sequence"); // Create sequence column header if
+ tableModel.addColumn("Ref Sequence"); // Create sequence column header if
// exists in the request
}
for (PDBDocField field : request.getWantedFields())
// exists in the request
}
for (PDBDocField field : request.getWantedFields())
@@
-127,16
+128,16
@@
public class PDBRestResponse
{
private String pdbId;
{
private String pdbId;
- private String[] summaryRowData;
+ private Object[] summaryRowData;
- private String associatedSequence;
+ private SequenceI associatedSequence;
public PDBResponseSummary(JSONObject pdbJsonDoc, PDBRestRequest request)
{
Collection<PDBDocField> diplayFields = request.getWantedFields();
public PDBResponseSummary(JSONObject pdbJsonDoc, PDBRestRequest request)
{
Collection<PDBDocField> diplayFields = request.getWantedFields();
- String associatedSeq = request.getAssociatedSequence();
+ SequenceI associatedSeq = request.getAssociatedSequence();
int colCounter = 0;
int colCounter = 0;
- summaryRowData = new String[(associatedSeq != null) ? diplayFields
+ summaryRowData = new Object[(associatedSeq != null) ? diplayFields
.size() + 1 : diplayFields.size()];
if (associatedSeq != null)
{
.size() + 1 : diplayFields.size()];
if (associatedSeq != null)
{
@@
-172,7
+173,7
@@
public class PDBRestResponse
this.pdbId = pdbId;
}
this.pdbId = pdbId;
}
- public String[] getSummaryData()
+ public Object[] getSummaryData()
{
return summaryRowData;
}
{
return summaryRowData;
}
@@
-189,9
+190,9
@@
public class PDBRestResponse
public String toString()
{
StringBuilder summaryFieldValues = new StringBuilder();
public String toString()
{
StringBuilder summaryFieldValues = new StringBuilder();
- for (String summaryField : summaryRowData)
+ for (Object summaryField : summaryRowData)
{
{
- summaryFieldValues.append(summaryField).append("\t");
+ summaryFieldValues.append(summaryField.toString()).append("\t");
}
return summaryFieldValues.toString();
}
}
return summaryFieldValues.toString();
}