From 8200f192900c29a55614b0266d84169b1688af92 Mon Sep 17 00:00:00 2001
From: tcarver <tjc>
Date: Fri, 31 Aug 2012 12:26:07 +0100
Subject: [PATCH] tidy
---
.../artemis/components/alignment/BamView.java | 117 ++++++++----------
1 file changed, 50 insertions(+), 67 deletions(-)
diff --git a/uk/ac/sanger/artemis/components/alignment/BamView.java b/uk/ac/sanger/artemis/components/alignment/BamView.java
index 3ef3b269c..4802e10f4 100644
--- a/uk/ac/sanger/artemis/components/alignment/BamView.java
+++ b/uk/ac/sanger/artemis/components/alignment/BamView.java
@@ -527,23 +527,17 @@ public class BamView extends JPanel
private void readHeaderPicard() throws IOException
{
- String bam = bamList.get(0);
- final SAMFileReader inputSam = getSAMFileReader(bam);
-
- //final SAMFileReader inputSam = new SAMFileReader(bamFile, indexFile);
- SAMFileHeader header = inputSam.getFileHeader();
- List<SAMSequenceRecord> readGroups = header.getSequenceDictionary().getSequences();
-
- for(int i=0; i<readGroups.size(); i++)
+ final SAMFileReader inputSam = getSAMFileReader(bamList.get(0));
+ final SAMFileHeader header = inputSam.getFileHeader();
+
+ for(SAMSequenceRecord seq: header.getSequenceDictionary().getSequences())
{
- seqLengths.put(readGroups.get(i).getSequenceName(),
- readGroups.get(i).getSequenceLength());
- seqNames.add(readGroups.get(i).getSequenceName());
+ seqLengths.put(seq.getSequenceName(),
+ seq.getSequenceLength());
+ seqNames.add(seq.getSequenceName());
}
- //inputSam.close();
}
-
/**
* Read a SAM or BAM file.
* @throws IOException
@@ -553,16 +547,16 @@ public class BamView extends JPanel
{
// Open the input file. Automatically detects whether input is SAM or BAM
// and delegates to a reader implementation for the appropriate format.
- String bam = bamList.get(bamIndex);
+ final String bam = bamList.get(bamIndex);
final SAMFileReader inputSam = getSAMFileReader(bam);
//final SAMFileReader inputSam = new SAMFileReader(bamFile, indexFile);
if(isConcatSequences())
{
- for(int i=0; i<seqNames.size(); i++)
+ for(String seq: seqNames)
{
- int sLen = seqLengths.get(seqNames.get(i));
- int offset = getSequenceOffset(seqNames.get(i));
+ int sLen = seqLengths.get(seq);
+ int offset = getSequenceOffset(seq);
int sBeg = offset+1;
int sEnd = sBeg+sLen-1;
@@ -576,8 +570,8 @@ public class BamView extends JPanel
if(thisEnd > sLen)
thisEnd = sLen;
- iterateOverBam(inputSam, seqNames.get(i), thisStart, thisEnd, bamIndex, pixPerBase, bam);
- //System.out.println("READ "+seqNames.get(i)+" "+thisStart+".."+thisEnd+" "+start+" --- "+offset);
+ iterateOverBam(inputSam, seq, thisStart, thisEnd, bamIndex, pixPerBase, bam);
+ //System.out.println("READ "+seq+" "+thisStart+".."+thisEnd+" "+start+" --- "+offset);
}
}
}
@@ -586,7 +580,6 @@ public class BamView extends JPanel
String refName = (String) combo.getSelectedItem();
iterateOverBam(inputSam, refName, start, end, bamIndex, pixPerBase, bam);
}
-
//inputSam.close();
}
@@ -605,7 +598,7 @@ public class BamView extends JPanel
{
final CloseableIterator<SAMRecord> it = inputSam.queryOverlapping(refName, start, end);
MemoryMXBean memory = ManagementFactory.getMemoryMXBean();
- int checkMemAfter = 8000;
+ final int checkMemAfter = 8000;
int cnt = 0;
final int seqOffset = getSequenceOffset(refName);
final int offset = seqOffset- getBaseAtStartOfView();
@@ -676,8 +669,8 @@ public class BamView extends JPanel
if(isConcatSequences())
{
int len = 0;
- for(int i=0; i<seqNames.size(); i++)
- len += seqLengths.get(seqNames.get(i));
+ for(String seq: seqNames)
+ len += seqLengths.get(seq);
return len;
}
else
@@ -768,7 +761,7 @@ public class BamView extends JPanel
Graphics2D g2 = (Graphics2D)g;
mouseOverSAMRecord = null;
- int seqLength = getSequenceLength();
+ final int seqLength = getSequenceLength();
int start;
int end;
@@ -789,7 +782,7 @@ public class BamView extends JPanel
nbasesInView = feature_display.getMaxVisibleBases();
}
- float pixPerBase = getPixPerBaseByWidth();
+ final float pixPerBase = getPixPerBaseByWidth();
boolean changeToStackView = false;
MemoryMXBean memory = ManagementFactory.getMemoryMXBean();
if(laststart != start ||
@@ -809,7 +802,6 @@ public class BamView extends JPanel
{
float heapFractionUsedBefore = (float) ((float) memory.getHeapMemoryUsage().getUsed() /
(float) memory.getHeapMemoryUsage().getMax());
-
if(readsInView == null)
readsInView = new Vector<BamViewRecord>();
else
@@ -1192,11 +1184,11 @@ public class BamView extends JPanel
if(isShowScale())
drawScale(g2, start, end, pixPerBase, getHeight());
- Stroke stroke =
+ final Stroke stroke =
new BasicStroke (1.3f, BasicStroke.CAP_BUTT, BasicStroke.JOIN_ROUND);
g2.setStroke(stroke);
- int scaleHeight;
+ final int scaleHeight;
if(isShowScale())
scaleHeight = 15;
else
@@ -1282,17 +1274,13 @@ public class BamView extends JPanel
private int getYPos(int scaleHeight, int size)
{
- int ypos;
-
if(!logScale)
- ypos = (getHeight() - scaleHeight) - size;
+ return (getHeight() - scaleHeight) - size;
else
{
int logInfSize = (int)( Math.log(size) * 100);
- ypos = (getHeight() - scaleHeight) - logInfSize;
+ return (getHeight() - scaleHeight) - logInfSize;
}
-
- return ypos;
}
/**
@@ -1310,22 +1298,22 @@ public class BamView extends JPanel
* @param end
*/
private void drawStackView(Graphics2D g2,
- int seqLength,
- float pixPerBase,
- int start,
- int end)
+ final int seqLength,
+ final float pixPerBase,
+ final int start,
+ final int end)
{
drawSelectionRange(g2, pixPerBase,start, end, Color.PINK);
if(isShowScale())
drawScale(g2, start, end, pixPerBase, getHeight());
- BasicStroke stroke = new BasicStroke(
+ final BasicStroke stroke = new BasicStroke(
1.3f,
BasicStroke.CAP_BUTT,
BasicStroke.JOIN_MITER);
g2.setStroke(stroke);
- int scaleHeight;
+ final int scaleHeight;
if(isShowScale())
scaleHeight = 15;
else
@@ -1338,13 +1326,12 @@ public class BamView extends JPanel
int maxEnd = 0;
int lstStart = 0;
int lstEnd = 0;
- int baseAtStartOfView = getBaseAtStartOfView();
+ final int baseAtStartOfView = getBaseAtStartOfView();
g2.setColor(Color.blue);
- Rectangle r = jspView.getViewport().getViewRect();
+ final Rectangle r = jspView.getViewport().getViewRect();
- for(int i=0; i<readsInView.size(); i++)
+ for(BamViewRecord bamViewRecord: readsInView)
{
- BamViewRecord bamViewRecord = readsInView.get(i);
SAMRecord samRecord = bamViewRecord.sam;
int offset = getSequenceOffset(samRecord.getReferenceName());
@@ -1403,12 +1390,12 @@ public class BamView extends JPanel
int end)
{
drawSelectionRange(g2, pixPerBase,start, end, Color.PINK);
- BasicStroke stroke = new BasicStroke(
+ final BasicStroke stroke = new BasicStroke(
1.3f,
BasicStroke.CAP_BUTT,
BasicStroke.JOIN_MITER);
- int scaleHeight = 15;
+ final int scaleHeight = 15;
drawScale(g2, start, end, pixPerBase, ((getHeight()+scaleHeight)/2));
int ymid = (getHeight()/ 2);
@@ -1439,15 +1426,14 @@ public class BamView extends JPanel
g2.setColor(Color.blue);
Rectangle r = jspView.getViewport().getViewRect();
- for(int i=0; i<readsInView.size(); i++)
+ for(BamViewRecord bamViewRecord: readsInView)
{
- BamViewRecord bamViewRecord = readsInView.get(i);
SAMRecord samRecord = bamViewRecord.sam;
if( samRecord.getReadNegativeStrandFlag() == isStrandNegative )
{
- int offset = getSequenceOffset(samRecord.getReferenceName());
- int recordStart = samRecord.getAlignmentStart()+offset;
- int recordEnd = samRecord.getAlignmentEnd()+offset;
+ final int offset = getSequenceOffset(samRecord.getReferenceName());
+ final int recordStart = samRecord.getAlignmentStart()+offset;
+ final int recordEnd = samRecord.getAlignmentEnd()+offset;
if(colourByCoverageColour.isSelected() ||
lstStart != recordStart || lstEnd != recordEnd)
@@ -1490,10 +1476,10 @@ public class BamView extends JPanel
* @param end
*/
private void drawPairedStackView(Graphics2D g2,
- int seqLength,
- float pixPerBase,
- int start,
- int end)
+ final int seqLength,
+ final float pixPerBase,
+ final int start,
+ final int end)
{
drawSelectionRange(g2, pixPerBase,start, end, Color.PINK);
if(isShowScale())
@@ -1546,7 +1532,7 @@ public class BamView extends JPanel
new BasicStroke (1.3f, BasicStroke.CAP_BUTT, BasicStroke.JOIN_ROUND);
g2.setStroke(stroke);
- int scaleHeight;
+ final int scaleHeight;
if(isShowScale())
scaleHeight = 15;
else
@@ -1560,9 +1546,8 @@ public class BamView extends JPanel
int baseAtStartOfView = getBaseAtStartOfView();
Rectangle r = jspView.getViewport().getViewRect();
- for(int i=0; i<pairedReads.size(); i++)
+ for(PairedRead pr: pairedReads)
{
- PairedRead pr = pairedReads.get(i);
if(pr.sam1.sam.getAlignmentStart() > lastEnd)
{
ypos = getHeight() - scaleHeight - ydiff;
@@ -1869,10 +1854,11 @@ public class BamView extends JPanel
* @param ypos
* @param baseAtStartOfView
*/
- private void drawRead(Graphics2D g2, SAMRecord thisRead,
- float pixPerBase,
- int ypos,
- int baseAtStartOfView)
+ private void drawRead(Graphics2D g2,
+ final SAMRecord thisRead,
+ final float pixPerBase,
+ final int ypos,
+ final int baseAtStartOfView)
{
int offset = getSequenceOffset(thisRead.getReferenceName());
@@ -2048,7 +2034,6 @@ public class BamView extends JPanel
// use alignment blocks of the contiguous alignment of
// subsets of read bases to a reference sequence
- List<AlignmentBlock> blocks = thisRead.getAlignmentBlocks();
try
{
char[] refSeq = bases.getSubSequenceC(
@@ -2059,9 +2044,9 @@ public class BamView extends JPanel
g2.setColor(Color.red);
offset = offset - getBaseAtStartOfView();
- for(int i=0; i<blocks.size(); i++)
+ final List<AlignmentBlock> blocks = thisRead.getAlignmentBlocks();
+ for(AlignmentBlock block: blocks)
{
- AlignmentBlock block = blocks.get(i);
for(int j=0; j<block.getLength(); j++)
{
int readPos = block.getReadStart()-1+j;
@@ -2073,9 +2058,7 @@ public class BamView extends JPanel
(int) ((refPos+offset) * pixPerBase), ypos - 2);
}
}
-
}
-
g2.setColor(col);
}
catch (OutOfRangeException e)
--
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