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JAL-3285 fix incorrect file paths on HMMAlign/Search results
author
tva
<tva@10.205.251.175>
Thu, 6 Jun 2019 14:28:52 +0000
(15:28 +0100)
committer
tva
<tva@10.205.251.175>
Thu, 6 Jun 2019 14:28:52 +0000
(15:28 +0100)
src/jalview/hmmer/HMMAlign.java
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src/jalview/hmmer/HMMBuild.java
patch
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src/jalview/hmmer/HMMSearch.java
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src/jalview/hmmer/HmmerCommand.java
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diff --git
a/src/jalview/hmmer/HMMAlign.java
b/src/jalview/hmmer/HMMAlign.java
index
b5f047e
..
57e35e7
100644
(file)
--- a/
src/jalview/hmmer/HMMAlign.java
+++ b/
src/jalview/hmmer/HMMAlign.java
@@
-152,9
+152,9
@@
public class HMMAlign extends HmmerCommand
}
}
args.add("-o");
}
}
args.add("-o");
- args.add(getFilePath(resultFile));
- args.add(getFilePath(modelFile));
- args.add(getFilePath(alignmentFile));
+ args.add(getFilePath(resultFile, true));
+ args.add(getFilePath(modelFile, true));
+ args.add(getFilePath(alignmentFile, true));
return runCommand(args);
}
return runCommand(args);
}
@@
-172,7
+172,7
@@
public class HMMAlign extends HmmerCommand
private SequenceI[] importData(File resultFile,
List<AlignmentOrder> allOrders) throws IOException
{
private SequenceI[] importData(File resultFile,
List<AlignmentOrder> allOrders) throws IOException
{
- StockholmFile file = new StockholmFile(getFilePath(resultFile),
+ StockholmFile file = new StockholmFile(getFilePath(resultFile, false),
DataSourceType.FILE);
SequenceI[] result = file.getSeqsAsArray();
AlignmentOrder msaorder = new AlignmentOrder(result);
DataSourceType.FILE);
SequenceI[] result = file.getSeqsAsArray();
AlignmentOrder msaorder = new AlignmentOrder(result);
diff --git
a/src/jalview/hmmer/HMMBuild.java
b/src/jalview/hmmer/HMMBuild.java
index
ee133ff
..
0b6e3ee
100644
(file)
--- a/
src/jalview/hmmer/HMMBuild.java
+++ b/
src/jalview/hmmer/HMMBuild.java
@@
-334,8
+334,8
@@
public class HMMBuild extends HmmerCommand
args.add(ARG_DNA);
}
args.add(ARG_DNA);
}
- args.add(getFilePath(hmmFile));
- args.add(getFilePath(sequencesFile));
+ args.add(getFilePath(hmmFile, true));
+ args.add(getFilePath(sequencesFile, true));
return runCommand(args);
}
return runCommand(args);
}
diff --git
a/src/jalview/hmmer/HMMSearch.java
b/src/jalview/hmmer/HMMSearch.java
index
1883fef
..
3773e84
100644
(file)
--- a/
src/jalview/hmmer/HMMSearch.java
+++ b/
src/jalview/hmmer/HMMSearch.java
@@
-181,9
+181,9
@@
public class HMMSearch extends HmmerCommand
File hitsAlignmentFile, File hmmFile) throws IOException
{
args.add("-o");
File hitsAlignmentFile, File hmmFile) throws IOException
{
args.add("-o");
- args.add(getFilePath(searchOutputFile));
+ args.add(getFilePath(searchOutputFile, true));
args.add("-A");
args.add("-A");
- args.add(getFilePath(hitsAlignmentFile));
+ args.add(getFilePath(hitsAlignmentFile, true));
boolean dbFound = false;
String dbPath = "";
boolean dbFound = false;
String dbPath = "";
@@
-314,8
+314,8
@@
public class HMMSearch extends HmmerCommand
exportStockholm(copy.getSequencesArray(), databaseFile, null);
}
exportStockholm(copy.getSequencesArray(), databaseFile, null);
}
- args.add(getFilePath(hmmFile));
- args.add(getFilePath(databaseFile));
+ args.add(getFilePath(hmmFile, true));
+ args.add(getFilePath(databaseFile, true));
}
/**
}
/**
diff --git
a/src/jalview/hmmer/HmmerCommand.java
b/src/jalview/hmmer/HmmerCommand.java
index
73995af
..
20e0083
100644
(file)
--- a/
src/jalview/hmmer/HmmerCommand.java
+++ b/
src/jalview/hmmer/HmmerCommand.java
@@
-257,7
+257,8
@@
public abstract class HmmerCommand implements Runnable
* @return
* @throws IOException
*/
* @return
* @throws IOException
*/
- protected String getCommandPath(String cmd) throws IOException
+ protected String getCommandPath(String cmd)
+ throws IOException
{
String binariesFolder = Cache.getProperty(Preferences.HMMER_PATH);
// ensure any symlink to the directory is resolved:
{
String binariesFolder = Cache.getProperty(Preferences.HMMER_PATH);
// ensure any symlink to the directory is resolved:
@@
-269,7
+270,7
@@
public abstract class HmmerCommand implements Runnable
.formatMessage("label.executable_not_found", cmd));
}
.formatMessage("label.executable_not_found", cmd));
}
- return file == null ? null : getFilePath(file);
+ return file == null ? null : getFilePath(file, true);
}
/**
}
/**
@@
-323,12
+324,15
@@
public abstract class HmmerCommand implements Runnable
* X with /cygdrive/x.
*
* @param resultFile
* X with /cygdrive/x.
*
* @param resultFile
+ * @param isInCygwin
+ * True if file is to be read/written from within the Cygwin
+ * shell. Should be false for any imports.
* @return
*/
* @return
*/
- protected String getFilePath(File resultFile)
+ protected String getFilePath(File resultFile, boolean isInCygwin)
{
String path = resultFile.getAbsolutePath();
{
String path = resultFile.getAbsolutePath();
- if (Platform.isWindows())
+ if (Platform.isWindows() && isInCygwin)
{
// the first backslash escapes '\' for the regular expression argument
path = path.replaceAll("\\" + File.separator, "/");
{
// the first backslash escapes '\' for the regular expression argument
path = path.replaceAll("\\" + File.separator, "/");