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JAL-3878 Create web service class - container for service metadata and actions
[jalview.git]
/
src
/
jalview
/
hmmer
/
HmmerCommand.java
diff --git
a/src/jalview/hmmer/HmmerCommand.java
b/src/jalview/hmmer/HmmerCommand.java
index
b311b76
..
e241008
100644
(file)
--- a/
src/jalview/hmmer/HmmerCommand.java
+++ b/
src/jalview/hmmer/HmmerCommand.java
@@
-1,6
+1,7
@@
package jalview.hmmer;
import jalview.analysis.SeqsetUtils;
package jalview.hmmer;
import jalview.analysis.SeqsetUtils;
+import jalview.analysis.SeqsetUtils.SequenceInfo;
import jalview.bin.Cache;
import jalview.datamodel.Alignment;
import jalview.datamodel.AlignmentAnnotation;
import jalview.bin.Cache;
import jalview.datamodel.Alignment;
import jalview.datamodel.AlignmentAnnotation;
@@
-30,6
+31,7
@@
import java.nio.file.Paths;
import java.util.ArrayList;
import java.util.Hashtable;
import java.util.List;
import java.util.ArrayList;
import java.util.Hashtable;
import java.util.List;
+import java.util.Map;
/**
* Base class for hmmbuild, hmmalign and hmmsearch
/**
* Base class for hmmbuild, hmmalign and hmmsearch
@@
-127,7
+129,7
@@
public abstract class HmmerCommand implements Runnable
*
* @param seqs
*/
*
* @param seqs
*/
- protected Hashtable stashSequences(SequenceI[] seqs)
+ protected Map<String, SequenceInfo> stashSequences(SequenceI[] seqs)
{
return SeqsetUtils.uniquify(seqs, true);
}
{
return SeqsetUtils.uniquify(seqs, true);
}
@@
-135,12
+137,12
@@
public abstract class HmmerCommand implements Runnable
/**
* Restores the sequence data lost by uniquifying
*
/**
* Restores the sequence data lost by uniquifying
*
- * @param hashtable
+ * @param sequencesHash
* @param seqs
*/
* @param seqs
*/
- protected void recoverSequences(Hashtable hashtable, SequenceI[] seqs)
+ protected void recoverSequences(Map<String, SequenceInfo> sequencesHash, SequenceI[] seqs)
{
{
- SeqsetUtils.deuniquify(hashtable, seqs);
+ SeqsetUtils.deuniquify(sequencesHash, seqs);
}
/**
}
/**
@@
-154,14
+156,14
@@
public abstract class HmmerCommand implements Runnable
public boolean runCommand(List<String> commands)
throws IOException
{
public boolean runCommand(List<String> commands)
throws IOException
{
- List<String> args = Platform.isWindows() ? wrapWithCygwin(commands)
+ List<String> args = Platform.isWindowsAndNotJS() ? wrapWithCygwin(commands)
: commands;
try
{
ProcessBuilder pb = new ProcessBuilder(args);
pb.redirectErrorStream(true); // merge syserr to sysout
: commands;
try
{
ProcessBuilder pb = new ProcessBuilder(args);
pb.redirectErrorStream(true); // merge syserr to sysout
- if (Platform.isWindows())
+ if (Platform.isWindowsAndNotJS())
{
String path = pb.environment().get("Path");
path = jalview.bin.Cache.getProperty("CYGWIN_PATH") + ";" + path;
{
String path = pb.environment().get("Path");
path = jalview.bin.Cache.getProperty("CYGWIN_PATH") + ";" + path;
@@
-436,7
+438,7
@@
public abstract class HmmerCommand implements Runnable
protected String getFilePath(File resultFile, boolean isInCygwin)
{
String path = resultFile.getAbsolutePath();
protected String getFilePath(File resultFile, boolean isInCygwin)
{
String path = resultFile.getAbsolutePath();
- if (Platform.isWindows() && isInCygwin)
+ if (Platform.isWindowsAndNotJS() && 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, "/");