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JAL-3113 override minimum frame size in a way that works in JalviewJS
[jalview.git]
/
src
/
jalview
/
io
/
StructureFile.java
diff --git
a/src/jalview/io/StructureFile.java
b/src/jalview/io/StructureFile.java
index
40bb8be
..
16ae0a1
100644
(file)
--- a/
src/jalview/io/StructureFile.java
+++ b/
src/jalview/io/StructureFile.java
@@
-38,7
+38,7
@@
import java.lang.reflect.Constructor;
import java.util.List;
import java.util.Vector;
import java.util.List;
import java.util.Vector;
-import MCview.PDBChain;
+import mc_view.PDBChain;
public abstract class StructureFile extends AlignFile
{
public abstract class StructureFile extends AlignFile
{
@@
-68,7
+68,7
@@
public abstract class StructureFile extends AlignFile
private boolean pdbIdAvailable;
private boolean pdbIdAvailable;
- public StructureFile(String inFile, DataSourceType sourceType)
+ public StructureFile(Object inFile, DataSourceType sourceType)
throws IOException
{
super(inFile, sourceType);
throws IOException
{
super(inFile, sourceType);
@@
-98,7
+98,7
@@
public abstract class StructureFile extends AlignFile
}
}
- public StructureFile(boolean parseImmediately, String dataObject,
+ public StructureFile(boolean parseImmediately, Object dataObject,
DataSourceType sourceType) throws IOException
{
super(parseImmediately, dataObject, sourceType);
DataSourceType sourceType) throws IOException
{
super(parseImmediately, dataObject, sourceType);
@@
-397,8
+397,10
@@
public abstract class StructureFile extends AlignFile
public static boolean isRNA(SequenceI seq)
{
public static boolean isRNA(SequenceI seq)
{
- for (char c : seq.getSequence())
+ int length = seq.getLength();
+ for (int i = 0; i < length; i++)
{
{
+ char c = seq.getCharAt(i);
if ((c != 'A') && (c != 'C') && (c != 'G') && (c != 'U'))
{
return false;
if ((c != 'A') && (c != 'C') && (c != 'G') && (c != 'U'))
{
return false;