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JAL-4366 compute coverage on each side of the pairwise alignment
[jalview.git]
/
src
/
jalview
/
ws
/
DBRefFetcher.java
diff --git
a/src/jalview/ws/DBRefFetcher.java
b/src/jalview/ws/DBRefFetcher.java
index
9420465
..
d108d4d
100644
(file)
--- a/
src/jalview/ws/DBRefFetcher.java
+++ b/
src/jalview/ws/DBRefFetcher.java
@@
-31,10
+31,13
@@
import java.util.List;
import java.util.Map;
import java.util.StringTokenizer;
import java.util.Vector;
import java.util.Map;
import java.util.StringTokenizer;
import java.util.Vector;
+import java.util.regex.Matcher;
+import java.util.regex.Pattern;
import jalview.analysis.AlignSeq;
import jalview.api.FeatureSettingsModelI;
import jalview.bin.Cache;
import jalview.analysis.AlignSeq;
import jalview.api.FeatureSettingsModelI;
import jalview.bin.Cache;
+import jalview.bin.Console;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.DBRefEntry;
import jalview.datamodel.DBRefSource;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.DBRefEntry;
import jalview.datamodel.DBRefSource;
@@
-299,12
+302,12
@@
public class DBRefFetcher implements Runnable
}
} catch (Exception e)
{
}
} catch (Exception e)
{
- System.err.println("Couldn't locate PICR service instance.\n");
+ jalview.bin.Console
+ .errPrintln("Couldn't locate PICR service instance.\n");
e.printStackTrace();
}
e.printStackTrace();
}
- Vector<SequenceI> sdataset = new Vector<>(
- Arrays.asList(dataset));
+ Vector<SequenceI> sdataset = new Vector<>(Arrays.asList(dataset));
List<String> warningMessages = new ArrayList<>();
// clear any old feature display settings recorded from past sessions
List<String> warningMessages = new ArrayList<>();
// clear any old feature display settings recorded from past sessions
@@
-314,7
+317,8
@@
public class DBRefFetcher implements Runnable
while (sdataset.size() > 0 && db < dbSources.length)
{
int maxqlen = 1; // default number of queries made at one time
while (sdataset.size() > 0 && db < dbSources.length)
{
int maxqlen = 1; // default number of queries made at one time
- System.out.println("Verifying against " + dbSources[db].getDbName());
+ jalview.bin.Console
+ .outPrintln("Verifying against " + dbSources[db].getDbName());
// iterate through db for each remaining un-verified sequence
SequenceI[] currSeqs = new SequenceI[sdataset.size()];
// iterate through db for each remaining un-verified sequence
SequenceI[] currSeqs = new SequenceI[sdataset.size()];
@@
-360,10
+364,10
@@
public class DBRefFetcher implements Runnable
AlignmentI retrieved = null;
try
{
AlignmentI retrieved = null;
try
{
- if (Cache.log.isDebugEnabled())
+ if (Console.isDebugEnabled())
{
{
- Cache.log.debug("Querying " + dbsource.getDbName()
- + " with : '" + queryString.toString() + "'");
+ Console.debug("Querying " + dbsource.getDbName() + " with : '"
+ + queryString.toString() + "'");
}
retrieved = dbsource.getSequenceRecords(queryString.toString());
} catch (Exception ex)
}
retrieved = dbsource.getSequenceRecords(queryString.toString());
} catch (Exception ex)
@@
-376,8
+380,8
@@
public class DBRefFetcher implements Runnable
}
if (retrieved != null)
{
}
if (retrieved != null)
{
- transferReferences(sdataset, dbsource, retrieved,
- trimDsSeqs, warningMessages);
+ transferReferences(sdataset, dbsource, retrieved, trimDsSeqs,
+ warningMessages);
}
}
else
}
}
else
@@
-396,7
+400,7
@@
public class DBRefFetcher implements Runnable
{
for (int j = 0, n = uprefs.size(); j < n; j++)
{
{
for (int j = 0, n = uprefs.size(); j < n; j++)
{
- DBRefEntry upref = uprefs.get(j);
+ DBRefEntry upref = uprefs.get(j);
addSeqId(sequence, upref.getAccessionId());
queries.addElement(
upref.getAccessionId().toUpperCase(Locale.ROOT));
addSeqId(sequence, upref.getAccessionId());
queries.addElement(
upref.getAccessionId().toUpperCase(Locale.ROOT));
@@
-404,12
+408,14
@@
public class DBRefFetcher implements Runnable
}
else
{
}
else
{
+ Pattern possibleIds = Pattern.compile("[A-Za-z0-9_]+");
// generate queries from sequence ID string
// generate queries from sequence ID string
- StringTokenizer st = new StringTokenizer(sequence.getName(),
- "|");
- while (st.hasMoreTokens())
+ Matcher tokens = possibleIds.matcher(sequence.getName());
+ int p = 0;
+ while (tokens.find(p))
{
{
- String token = st.nextToken();
+ String token = tokens.group();
+ p = tokens.end();
UPEntry[] presp = null;
if (picrClient != null)
{
UPEntry[] presp = null;
if (picrClient != null)
{
@@
-421,7
+427,7
@@
public class DBRefFetcher implements Runnable
true);
} catch (Exception e)
{
true);
} catch (Exception e)
{
- System.err.println(
+ jalview.bin.Console.errPrintln(
"Exception with Picr for '" + token + "'\n");
e.printStackTrace();
}
"Exception with Picr for '" + token + "'\n");
e.printStackTrace();
}
@@
-434,7
+440,7
@@
public class DBRefFetcher implements Runnable
// present, and do a transferReferences
// otherwise transfer non sequence x-references directly.
}
// present, and do a transferReferences
// otherwise transfer non sequence x-references directly.
}
- System.out.println(
+ jalview.bin.Console.outPrintln(
"Validated ID against PICR... (for what its worth):"
+ token);
addSeqId(sequence, token);
"Validated ID against PICR... (for what its worth):"
+ token);
addSeqId(sequence, token);
@@
-443,7
+449,7
@@
public class DBRefFetcher implements Runnable
else
{
// if ()
else
{
// if ()
- // System.out.println("Not querying source with
+ // jalview.bin.Console.outPrintln("Not querying source with
// token="+token+"\n");
addSeqId(sequence, token);
queries.addElement(token.toUpperCase(Locale.ROOT));
// token="+token+"\n");
addSeqId(sequence, token);
queries.addElement(token.toUpperCase(Locale.ROOT));
@@
-505,11
+511,10
@@
public class DBRefFetcher implements Runnable
* a list of messages to add to
*/
boolean transferReferences(Vector<SequenceI> sdataset,
* a list of messages to add to
*/
boolean transferReferences(Vector<SequenceI> sdataset,
- DbSourceProxy dbSourceProxy,
- AlignmentI retrievedAl, boolean trimDatasetSeqs,
- List<String> warningMessages)
+ DbSourceProxy dbSourceProxy, AlignmentI retrievedAl,
+ boolean trimDatasetSeqs, List<String> warningMessages)
{
{
- // System.out.println("trimming ? " + trimDatasetSeqs);
+ // jalview.bin.Console.outPrintln("trimming ? " + trimDatasetSeqs);
if (retrievedAl == null || retrievedAl.getHeight() == 0)
{
return false;
if (retrievedAl == null || retrievedAl.getHeight() == 0)
{
return false;
@@
-539,7
+544,7
@@
public class DBRefFetcher implements Runnable
}
for (int j = 0, n = entryRefs.size(); j < n; j++)
{
}
for (int j = 0, n = entryRefs.size(); j < n; j++)
{
- DBRefEntry ref = entryRefs.get(j);
+ DBRefEntry ref = entryRefs.get(j);
String accessionId = ref.getAccessionId();
// match up on accessionId
if (seqRefs.containsKey(accessionId.toUpperCase(Locale.ROOT)))
String accessionId = ref.getAccessionId();
// match up on accessionId
if (seqRefs.containsKey(accessionId.toUpperCase(Locale.ROOT)))
@@
-675,8
+680,8
@@
public class DBRefFetcher implements Runnable
}
}
}
}
- System.out.println("Adding dbrefs to " + sequence.getName()
- + " from " + dbSource + " sequence : "
+ jalview.bin.Console.outPrintln("Adding dbrefs to "
+ + sequence.getName() + " from " + dbSource + " sequence : "
+ retrievedSeq.getName());
sequence.transferAnnotation(retrievedSeq, mp);
+ retrievedSeq.getName());
sequence.transferAnnotation(retrievedSeq, mp);
@@
-736,7
+741,8
@@
public class DBRefFetcher implements Runnable
.toUpperCase(Locale.ROOT);
int oldstrt = alseqs[alsq].getStart();
alseqs[alsq].setStart(sequence.getSequenceAsString()
.toUpperCase(Locale.ROOT);
int oldstrt = alseqs[alsq].getStart();
alseqs[alsq].setStart(sequence.getSequenceAsString()
- .toUpperCase(Locale.ROOT).indexOf(ngAlsq) + sequence.getStart());
+ .toUpperCase(Locale.ROOT).indexOf(ngAlsq)
+ + sequence.getStart());
if (oldstrt != alseqs[alsq].getStart())
{
alseqs[alsq].setEnd(
if (oldstrt != alseqs[alsq].getStart())
{
alseqs[alsq].setEnd(
@@
-777,15
+783,17
@@
public class DBRefFetcher implements Runnable
/**
*
/**
*
- * @return any feature settings associated with sources that have provided sequences
+ * @return any feature settings associated with sources that have provided
+ * sequences
*/
*/
- public List<FeatureSettingsModelI>getFeatureSettingsModels()
+ public List<FeatureSettingsModelI> getFeatureSettingsModels()
{
return featureDisplaySettings == null
? Arrays.asList(new FeatureSettingsModelI[0])
: Arrays.asList(featureDisplaySettings.values()
.toArray(new FeatureSettingsModelI[1]));
}
{
return featureDisplaySettings == null
? Arrays.asList(new FeatureSettingsModelI[0])
: Arrays.asList(featureDisplaySettings.values()
.toArray(new FeatureSettingsModelI[1]));
}
+
/**
* Adds the message to the list unless it already contains it
*
/**
* Adds the message to the list unless it already contains it
*
@@
-808,11
+816,11
@@
public class DBRefFetcher implements Runnable
*/
private SequenceI[] recoverDbSequences(SequenceI[] sequencesArray)
{
*/
private SequenceI[] recoverDbSequences(SequenceI[] sequencesArray)
{
- int n;
- if (sequencesArray == null || (n = sequencesArray.length) == 0)
- return sequencesArray;
+ int n;
+ if (sequencesArray == null || (n = sequencesArray.length) == 0)
+ return sequencesArray;
ArrayList<SequenceI> nseq = new ArrayList<>();
ArrayList<SequenceI> nseq = new ArrayList<>();
- for (int i = 0;i < n; i++)
+ for (int i = 0; i < n; i++)
{
nseq.add(sequencesArray[i]);
List<DBRefEntry> dbr = sequencesArray[i].getDBRefs();
{
nseq.add(sequencesArray[i]);
List<DBRefEntry> dbr = sequencesArray[i].getDBRefs();
@@
-827,11
+835,12
@@
public class DBRefFetcher implements Runnable
{
nseq.add(map.getTo());
}
{
nseq.add(map.getTo());
}
- }
+ }
}
}
}
}
}
}
- // BH 2019.01.25 question here if this is the right logic. Return the original if nothing found?
+ // BH 2019.01.25 question here if this is the right logic. Return the
+ // original if nothing found?
if (nseq.size() > 0)
{
return nseq.toArray(new SequenceI[nseq.size()]);
if (nseq.size() > 0)
{
return nseq.toArray(new SequenceI[nseq.size()]);