Java 17 changes

igvteam · Oct 19, 2023 · 0478c64 · 0478c64
1 parent 3156369
commit 0478c64
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Showing 2 changed files with 24 additions and 52 deletions.
diff --git a/src/main/java/org/broad/igv/sam/AlignmentRenderer.java b/src/main/java/org/broad/igv/sam/AlignmentRenderer.java
@@ -944,10 +944,10 @@ private static void drawClippedEnds(final Graphics2D g, final int[] xPoly, final
         try {
             //left side
             if (drawLeftClip) {
-                if (sri != null && sri.previous != null) {
-                    final SupplementaryAlignment previous = sri.previous;
-                    if (previous.contigsMatch(sri.alignment)) {
-                        g.setColor(previous.getStrand() == sri.alignment.getReadStrand() ? NON_INVERSION_COLOR : INVERSION_COLOR);
+                if (sri != null && sri.previous() != null) {
+                    final SupplementaryAlignment previous = sri.previous();
+                    if (previous.contigsMatch(sri.alignment())) {
+                        g.setColor(previous.getStrand() == sri.alignment().getReadStrand() ? NON_INVERSION_COLOR : INVERSION_COLOR);
                     } else {
                         if (previous.getContig() != null) {
                             g.setColor(ChromosomeColors.getColor(previous.getContig()));
@@ -969,11 +969,11 @@ private static void drawClippedEnds(final Graphics2D g, final int[] xPoly, final
             }
             //right side
             if (drawRightClip) {
-                if (sri != null && sri.next != null) {
-                    final SupplementaryAlignment next = sri.next;
-                    if (next.contigsMatch(sri.alignment)) {
+                if (sri != null && sri.next() != null) {
+                    final SupplementaryAlignment next = sri.next();
+                    if (next.contigsMatch(sri.alignment())) {
                         //TODO Set to scaled color by contig position
-                        g.setColor(next.getStrand() == sri.alignment.getReadStrand() ? NON_INVERSION_COLOR : INVERSION_COLOR);
+                        g.setColor(next.getStrand() == sri.alignment().getReadStrand() ? NON_INVERSION_COLOR : INVERSION_COLOR);
                     } else {
                         g.setColor(ChromosomeColors.getColor(next.getContig()));
                         rightContigLabel = next.getContig();

diff --git a/src/main/java/org/broad/igv/sam/SupplementaryAlignment.java b/src/main/java/org/broad/igv/sam/SupplementaryAlignment.java
@@ -7,7 +7,6 @@
 import htsjdk.samtools.util.Locatable;
 import org.broad.igv.Globals;
 import org.broad.igv.feature.Strand;
-import org.broad.igv.feature.genome.ChromosomeNameComparator;
 import org.broad.igv.feature.genome.Genome;
 import org.broad.igv.feature.genome.GenomeManager;
 import org.broad.igv.logging.LogManager;
@@ -17,11 +16,7 @@
 import java.util.Arrays;
 import java.util.Collections;
 import java.util.Comparator;
-import java.util.Iterator;
 import java.util.List;
-import java.util.Objects;
-import java.util.stream.Collectors;
-import java.util.stream.Stream;
 
 public class SupplementaryAlignment implements Locatable {
     private static final Logger log = LogManager.getLogger(SupplementaryAlignment.class);
@@ -145,14 +140,10 @@ public int getCountOfLeadingClipping(){
     }
 
     public static int getCountOfLeadingClipping(final ClippingCounts counts, final Strand strand) {
-        switch(strand){
-            case NONE:  // if there's no strand it's not aligned, and we can assume it's in cycle order
-            case POSITIVE:
-                return counts.getLeft();
-            case NEGATIVE:
-                return counts.getRight();
-            default: throw new IllegalStateException(strand + " is not an expected value for strand");
-        }
+        return switch (strand) {  // if there's no strand it's not aligned, and we can assume it's in cycle order
+            case NONE, POSITIVE -> counts.getLeft();
+            case NEGATIVE -> counts.getRight();
+        };
     }
 
     /**
@@ -186,21 +177,14 @@ public int getLengthOnReference() {
     /**
      * get the count of non-clipped bases which are in the read
      * this differs from {@link #getLengthOnReference()} because it includes insertions bases but not deletions
-     * @return
      */
     public int getNumberOfAlignedBases(){
         if( numberOfAlignedBases == null) {
             int length = 0;
             for(CigarElement element : cigar) {
                 switch (element.getOperator()) {
-                    case M:
-                    case I:
-                    case EQ:
-                    case X:
-                        length += element.getLength();
-                        break;
-                    default:
-                        break;
+                    case M, I, EQ, X -> length += element.getLength();
+                    default -> {}
                 }
             }
             numberOfAlignedBases = length;
@@ -209,30 +193,18 @@ public int getNumberOfAlignedBases(){
     }
 
 
-
-    static class SupplementaryNeighbors {
-        final Alignment alignment;
-        final SupplementaryAlignment previous;
-        final SupplementaryAlignment next;
-        public SupplementaryNeighbors(Alignment alignment,
-                                      SupplementaryAlignment previous, SupplementaryAlignment next) {
-            this.alignment = alignment;
-            if(alignment.isNegativeStrand()){
-                this.next = previous;
-                this.previous = next;
-            } else {
-                this.next = next;
-                this.previous = previous;
+    record SupplementaryNeighbors(Alignment alignment, SupplementaryAlignment previous, SupplementaryAlignment next) {
+            SupplementaryNeighbors(Alignment alignment, SupplementaryAlignment previous, SupplementaryAlignment next) {
+                this.alignment = alignment;
+                if (alignment.isNegativeStrand()) {
+                    this.next = previous;
+                    this.previous = next;
+                } else {
+                    this.next = next;
+                    this.previous = previous;
+                }
             }
-        }
-        public SupplementaryAlignment previousIgnoreOrientation (){
-            return alignment.isNegativeStrand() ? next : previous;
-        }
 
-        public SupplementaryAlignment nextIgnoreOrientation (){
-            return alignment.isNegativeStrand() ? previous : next;
         }
 
-    }
-
 }