Set default max RMSD for SmWat3D high to maintain default behavior

lafita · lafita · commit d2644ea6a48f · 2017-01-13T15:51:52.000+01:00
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/seq/SmithWaterman3DParameters.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/seq/SmithWaterman3DParameters.java
@@ -68,7 +68,7 @@ public List<String> getUserConfigParameters() {
 		List<String> params = new ArrayList<String>();
 		params.add("GapOpen");
 		params.add("GapExtend");
-		params.add("MaxRMSD");
+		params.add("MaxRmsd");
 		params.add("MinLen");
 		
 		return params;
@@ -90,7 +90,7 @@ public List<Class> getUserConfigTypes() {
 	public void reset() {
 		gapOpen = (short) 8;
 		gapExtend = (short) 1;
-		maxRmsd = 10.0;
+		maxRmsd = 99;
 		minLen = 30;
 
 	}
@@ -111,15 +111,15 @@ public void setGapOpen(Short gapOpen) {
 		this.gapOpen = gapOpen;
 	}
 
-	public double getMaxRmsd() {
+	public Double getMaxRmsd() {
 		return maxRmsd;
 	}
 
 	public void setMaxRmsd(Double maxRmsd) {
 		this.maxRmsd = maxRmsd;
 	}
 
-	public int getMinLen() {
+	public Integer getMinLen() {
 		return minLen;
 	}
 
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/util/AlignmentTools.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/util/AlignmentTools.java
@@ -1462,7 +1462,7 @@ public static AFPChain deleteColumn(AFPChain afpChain, Atom[] ca1,
 					"Block index requested (%d) is higher than the total number of AFPChain blocks (%d).",
 					block, afpChain.getBlockNum()));
 		}
-		if (afpChain.getBlockSize()[block] <= pos) {
+		if (afpChain.getOptAln()[block][0].length <= pos) {
 			throw new IndexOutOfBoundsException(String.format(
 					"Position index requested (%d) is higher than the total number of aligned position in the AFPChain block (%d).",
 					block, afpChain.getBlockSize()[block]));

Original file line number	Diff line number	Diff line change
`@@ -68,7 +68,7 @@ public List<String> getUserConfigParameters() {`
`68`	`68`	`List<String> params = new ArrayList<String>();`
`69`	`69`	`params.add("GapOpen");`
`70`	`70`	`params.add("GapExtend");`
`71`		`- params.add("MaxRMSD");`
	`71`	`+ params.add("MaxRmsd");`
`72`	`72`	`params.add("MinLen");`
`73`	`73`
`74`	`74`	`return params;`
`@@ -90,7 +90,7 @@ public List<Class> getUserConfigTypes() {`
`90`	`90`	`public void reset() {`
`91`	`91`	`gapOpen = (short) 8;`
`92`	`92`	`gapExtend = (short) 1;`
`93`		`- maxRmsd = 10.0;`
	`93`	`+ maxRmsd = 99;`
`94`	`94`	`minLen = 30;`
`95`	`95`
`96`	`96`	`}`
`@@ -111,15 +111,15 @@ public void setGapOpen(Short gapOpen) {`
`111`	`111`	`this.gapOpen = gapOpen;`
`112`	`112`	`}`
`113`	`113`
`114`		`- public double getMaxRmsd() {`
	`114`	`+ public Double getMaxRmsd() {`
`115`	`115`	`return maxRmsd;`
`116`	`116`	`}`
`117`	`117`
`118`	`118`	`public void setMaxRmsd(Double maxRmsd) {`
`119`	`119`	`this.maxRmsd = maxRmsd;`
`120`	`120`	`}`
`121`	`121`
`122`		`- public int getMinLen() {`
	`122`	`+ public Integer getMinLen() {`
`123`	`123`	`return minLen;`
`124`	`124`	`}`
`125`	`125`
Original file line number	Diff line number	Diff line change
`@@ -1462,7 +1462,7 @@ public static AFPChain deleteColumn(AFPChain afpChain, Atom[] ca1,`
`1462`	`1462`	`"Block index requested (%d) is higher than the total number of AFPChain blocks (%d).",`
`1463`	`1463`	`block, afpChain.getBlockNum()));`
`1464`	`1464`	`}`
`1465`		`- if (afpChain.getBlockSize()[block] <= pos) {`
	`1465`	`+ if (afpChain.getOptAln()[block][0].length <= pos) {`
`1466`	`1466`	`throw new IndexOutOfBoundsException(String.format(`
`1467`	`1467`	`"Position index requested (%d) is higher than the total number of aligned position in the AFPChain block (%d).",`
`1468`	`1468`	`block, afpChain.getBlockSize()[block]));`