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JAL-3253 temporary branch SwingJS upgrade with testNG fixes Java 8
[jalview.git]
/
src
/
jalview
/
io
/
TCoffeeScoreFile.java
diff --git
a/src/jalview/io/TCoffeeScoreFile.java
b/src/jalview/io/TCoffeeScoreFile.java
index
648954f
..
d069e5e
100644
(file)
--- a/
src/jalview/io/TCoffeeScoreFile.java
+++ b/
src/jalview/io/TCoffeeScoreFile.java
@@
-109,7
+109,7
@@
public class TCoffeeScoreFile extends AlignFile
public final static String TCOFFEE_SCORE = "TCoffeeScore";
public final static String TCOFFEE_SCORE = "TCoffeeScore";
- static Pattern SCORES_WITH_RESIDUE_NUMS = Pattern
+ private final static Pattern SCORES_WITH_RESIDUE_NUMS = Pattern
.compile("^\\d+\\s([^\\s]+)\\s+\\d+$");
/** The {@link Header} structure holder */
.compile("^\\d+\\s([^\\s]+)\\s+\\d+$");
/** The {@link Header} structure holder */
@@
-123,9
+123,10
@@
public class TCoffeeScoreFile extends AlignFile
Integer fWidth;
Integer fWidth;
- public TCoffeeScoreFile(String inFile, DataSourceType fileSourceType)
+ public TCoffeeScoreFile(Object inFile, DataSourceType fileSourceType)
throws IOException
{
throws IOException
{
+ // BH 2018 allows File or String
super(inFile, fileSourceType);
}
super(inFile, fileSourceType);
}
@@
-182,8
+183,9
@@
public class TCoffeeScoreFile extends AlignFile
*/
public String getScoresFor(String id)
{
*/
public String getScoresFor(String id)
{
- return scores != null && scores.containsKey(id) ? scores.get(id)
- .toString() : "";
+ return scores != null && scores.containsKey(id)
+ ? scores.get(id).toString()
+ : "";
}
/**
}
/**
@@
-196,7
+198,7
@@
public class TCoffeeScoreFile extends AlignFile
{
return null;
}
{
return null;
}
- List<String> result = new ArrayList<String>(scores.size());
+ List<String> result = new ArrayList<>(scores.size());
for (Map.Entry<String, StringBuilder> it : scores.entrySet())
{
result.add(it.getValue().toString());
for (Map.Entry<String, StringBuilder> it : scores.entrySet())
{
result.add(it.getValue().toString());
@@
-248,7
+250,7
@@
public class TCoffeeScoreFile extends AlignFile
error = true;
return;
}
error = true;
return;
}
- scores = new LinkedHashMap<String, StringBuilder>();
+ scores = new LinkedHashMap<>();
/*
* initilize the structure
/*
* initilize the structure
@@
-274,9
+276,9
@@
public class TCoffeeScoreFile extends AlignFile
if (scoreStringBuilder == null)
{
error = true;
if (scoreStringBuilder == null)
{
error = true;
- errormessage = String
- .format("Invalid T-Coffee score file: Sequence ID '%s' is not declared in header section",
- entry.getKey());
+ errormessage = String.format(
+ "Invalid T-Coffee score file: Sequence ID '%s' is not declared in header section",
+ entry.getKey());
return;
}
return;
}
@@
-501,7
+503,7
@@
public class TCoffeeScoreFile extends AlignFile
int score;
int score;
- LinkedHashMap<String, Integer> scores = new LinkedHashMap<String, Integer>();
+ LinkedHashMap<String, Integer> scores = new LinkedHashMap<>();
public int getScoreAvg()
{
public int getScoreAvg()
{
@@
-528,7
+530,7
@@
public class TCoffeeScoreFile extends AlignFile
public Block(int size)
{
this.size = size;
public Block(int size)
{
this.size = size;
- this.items = new HashMap<String, String>(size);
+ this.items = new HashMap<>(size);
}
String getScoresFor(String id)
}
String getScoresFor(String id)
@@
-584,9
+586,9
@@
public class TCoffeeScoreFile extends AlignFile
i++;
if (s == null && i != scores.size() && !id.getKey().equals("cons"))
{
i++;
if (s == null && i != scores.size() && !id.getKey().equals("cons"))
{
- System.err.println("No "
- + (matchids ? "match " : " sequences left ")
- + " for TCoffee score set : " + id.getKey());
+ System.err
+ .println("No " + (matchids ? "match " : " sequences left ")
+ + " for TCoffee score set : " + id.getKey());
continue;
}
int jSize = al.getWidth() < srow.length ? al.getWidth() : srow.length;
continue;
}
int jSize = al.getWidth() < srow.length ? al.getWidth() : srow.length;
@@
-599,16
+601,16
@@
public class TCoffeeScoreFile extends AlignFile
annotations[j] = null;
if (val > 0)
{
annotations[j] = null;
if (val > 0)
{
- System.err
- .println("Warning: non-zero value for positional T-COFFEE score for gap at "
+ System.err.println(
+ "Warning: non-zero value for positional T-COFFEE score for gap at "
+ j + " in sequence " + s.getName());
}
}
else
{
annotations[j] = new Annotation(s == null ? "" + val : null,
+ j + " in sequence " + s.getName());
}
}
else
{
annotations[j] = new Annotation(s == null ? "" + val : null,
- s == null ? "" + val : null, '\0', val * 1f, val >= 0
- && val < colors.length ? colors[val]
+ s == null ? "" + val : null, '\0', val * 1f,
+ val >= 0 && val < colors.length ? colors[val]
: Color.white);
}
}
: Color.white);
}
}