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Devel #5

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Merged
andreasprlic merged 3 commits into from
Apr 7, 2013
Merged

Devel #5

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379d6b2
removing eclipse warning
andreasprlic Apr 7, 2013
7811e48
removing eclipse warning
andreasprlic Apr 7, 2013
b039f34
cleanup of eclipse warnings
andreasprlic Apr 7, 2013
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1 change: 0 additions & 1 deletion biojava3-structure/src/main/java/org/biojava/bio/structure/Site.java
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Original file line number Diff line number Diff line change
Expand Up @@ -22,7 +22,6 @@

import java.io.Serializable;
import java.util.ArrayList;
import java.util.Formatter;
import java.util.List;
import java.util.Locale;

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3 changes: 3 additions & 0 deletions biojava3-structure/src/main/java/org/biojava/bio/structure/StructureTools.java
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Expand Up @@ -1043,6 +1043,7 @@ private static boolean isHbondDonorAcceptor(Atom atom) {
* @return a structure that contains only the first model
* @since 3.0.5
*/
@SuppressWarnings("deprecation")
public static Structure removeModels(Structure s){
if ( ! s.isNmr())
return s;
Expand All @@ -1055,6 +1056,8 @@ public static Structure removeModels(Structure s){

n.setPDBCode(s.getPDBCode());
n.setName(s.getName());

// we are calling this legacy menthod for backwards compatibility
n.setHeader(s.getHeader());
//TODO: do deep copying of data!
n.setPDBHeader(s.getPDBHeader());
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3 changes: 1 addition & 2 deletions ...a3-structure/src/main/java/org/biojava/bio/structure/align/StructureAlignmentFactory.java
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@@ -1,14 +1,12 @@
package org.biojava.bio.structure.align;

import java.lang.reflect.Constructor;
import java.util.ArrayList;
import java.util.List;
import java.util.ListIterator;

import org.biojava.bio.structure.StructureException;
import org.biojava.bio.structure.align.ce.CeCPMain;
import org.biojava.bio.structure.align.ce.CeMain;
import org.biojava.bio.structure.align.ce.OptimalCECPMain;
import org.biojava.bio.structure.align.fatcat.FatCatFlexible;
import org.biojava.bio.structure.align.fatcat.FatCatRigid;
import org.biojava.bio.structure.align.seq.SmithWaterman3Daligner;
Expand Down Expand Up @@ -82,6 +80,7 @@ public static void clearAlgorithms() {
algorithms.clear();
}

@SuppressWarnings("unchecked")
public static StructureAlignment getAlgorithm(String name) throws StructureException{
for ( StructureAlignment algo : algorithms){
if (algo.getAlgorithmName().equalsIgnoreCase(name)) {
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