Temporary commit. Needs to be amended!

Working Notes:

- Profile and LightweightProfile are too divergent currently. The
  formats are completely different. What is intended?
- Added toString(format, width) method, but some formats are fixed-width
  and should ignore this parameter and hard-code it.
- Added 'CONCENSUS' method with the idea that this would implement the
  request in biojava#983. However I'm not sure what the equivalent is in an MSA.
  Also the current version isn't actually the desired output.
- ProfileFormatTest is just a main method for quick testing

biojava-alignment/src/test/java/org/biojava/nbio/alignment/ProfileFormatTest.java

@@ -0,0 +1,80 @@
+package org.biojava.nbio.alignment;
+
+import java.util.Arrays;
+import java.util.Map;
+import java.util.function.Function;
+import java.util.stream.Collectors;
+
+import org.biojava.nbio.core.alignment.matrices.SubstitutionMatrixHelper;
+import org.biojava.nbio.core.alignment.template.AlignedSequence;
+import org.biojava.nbio.core.alignment.template.Profile;
+import org.biojava.nbio.core.alignment.template.SubstitutionMatrix;
+import org.biojava.nbio.core.exceptions.CompoundNotFoundException;
+import org.biojava.nbio.core.sequence.AccessionID;
+import org.biojava.nbio.core.sequence.ProteinSequence;
+import org.biojava.nbio.core.sequence.compound.AminoAcidCompound;
+import org.biojava.nbio.core.sequence.template.Sequence;
+
+public class ProfileFormatTest {
+
+    private static boolean isSimilar(SubstitutionMatrix<AminoAcidCompound> matrix, AminoAcidCompound aa1,
+            AminoAcidCompound aa2) {
+        short val = matrix.getValue(aa1, aa2);
+        return val > 0;
+    }
+
+    public static <S extends Sequence<C>, C extends AminoAcidCompound> String customFormat(
+            SmithWaterman<S, C> alignment) {
+        SubstitutionMatrix<AminoAcidCompound> blosum62 = SubstitutionMatrixHelper.getBlosum62();
+        AlignedSequence<S, C> seq1 = alignment.getPair().getAlignedSequence(1);
+        AlignedSequence<S, C> seq2 = alignment.getPair().getAlignedSequence(2);
+        String s1 = seq1.toString();
+        String s2 = seq2.toString();
+        String start1 = seq1.getStart().getPosition().toString();
+        String start2 = seq2.getStart().getPosition().toString();
+        int startWidth = Math.max(start1.length(), start2.length());
+
+        StringBuilder s = new StringBuilder();
+        s.append(String.format("%" + startWidth + "d ", seq1.getStart().getPosition()));
+        s.append(s1);
+        s.append(String.format(" %d", seq1.getEnd().getPosition()));
+        s.append(String.format("%n"));
+
+        s.append(String.format("%" + startWidth + "s", " "));
+        for (int i = 0; i < s1.toString().length(); i++) {
+            if (i >= s2.length())
+                break;
+
+            C c1 = seq1.getCompoundAt(i + 1);
+            C c2 = seq2.getCompoundAt(i + 1);
+            s.append(isSimilar(blosum62, c1, c2) ? '|' : ' ');
+        }
+        s.append(String.format("%n"));
+        s.append(String.format("%" + startWidth + "d ", seq2.getStart().getPosition()));
+        s.append(s2);
+        s.append(String.format(" %d", seq2.getEnd().getPosition()));
+
+        return s.toString();
+    }
+
+    public static void main(String[] args) throws CompoundNotFoundException {
+        // Test alignment
+        ProteinSequence query = new ProteinSequence("AERNDKK");
+        ProteinSequence target = new ProteinSequence("ERDNKGFPS");
+        query.setAccession(new AccessionID("query"));
+        target.setAccession(new AccessionID("target"));
+        SimpleGapPenalty gaps = new SimpleGapPenalty((short) 2, (short) 1);
+        SubstitutionMatrix<AminoAcidCompound> blosum62 = SubstitutionMatrixHelper.getBlosum62();
+        SmithWaterman<ProteinSequence, AminoAcidCompound> alignment = new SmithWaterman<ProteinSequence, AminoAcidCompound>(
+                query, target, gaps, blosum62);
+        String s = customFormat(alignment);
+
+        System.out.format("### custom:%n%s%n%n", s);
+        System.out.format("### toString:%n%s%n%n", alignment.getPair());
+
+        Map<Profile.StringFormat, String> fmts = Arrays.stream(Profile.StringFormat.values()).collect(
+                Collectors.toMap(Function.identity(), f -> alignment.getPair().toString(f)));
+        fmts.forEach((f, str) -> System.out.format("### %s:%n%s%n%n", f, str));
+
+    }
+}

biojava-core/src/main/java/org/biojava/nbio/core/alignment/SimpleProfile.java

@@ -37,6 +37,8 @@
 import org.biojava.nbio.core.sequence.template.Compound;
 import org.biojava.nbio.core.sequence.template.CompoundSet;
 import org.biojava.nbio.core.sequence.template.Sequence;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
 
 import java.io.Serializable;
 import java.util.*;
@@ -51,7 +53,7 @@
  * @param <C> each element of an {@link AlignedSequence} is a {@link Compound} of type C
  */
 public class SimpleProfile<S extends Sequence<C>, C extends Compound> implements Serializable, Profile<S, C> {
-
+	private static Logger logger = LoggerFactory.getLogger(SimpleProfile.class);
 
 	private static final long serialVersionUID = 1L;
 
@@ -376,25 +378,38 @@ public String toString(int width) {
 	}
 
 	@Override
-	public String toString(StringFormat format) {
+	public String toString(StringFormat format, int width) {
 		switch (format) {
+		default:
+			logger.warn("Unrecognized StringFormat {}", format);
+			// fall through
 		case ALN:
 		case CLUSTALW:
-		default:
-			return toString(60, String.format("CLUSTAL W MSA from BioJava%n%n"), IOUtils.getIDFormat(list) + "   ",
+			return toString(width, String.format("CLUSTAL W MSA from BioJava%n%n"), IOUtils.getIDFormat(list) + "   ",
 					false, true, true, false, true, false);
 		case FASTA:
-			return toString(60, null, ">%s%n", false, false, false, false, false, false);
+			return toString(width, null, ">%s%n", false, false, false, false, false, false);
 		case GCG:
 		case MSF:
-			return toString(50, IOUtils.getGCGHeader(list), IOUtils.getIDFormat(list), false, false, true, false,
+			return toString(width, IOUtils.getGCGHeader(list), IOUtils.getIDFormat(list), false, false, true, false,
 					false, false);
 		case PDBWEB:
-			return toString(60, null, "%10s", true, true, true, false, true, true);
+			return toString(width, null, "%10s", true, true, true, false, true, true);
+		case CONCENSUS:
+			return toString(width, null, null, false, true, true, false, true, false);
 		}
 	}
 
-	// method from Object
+	@Override
+	public String toString(StringFormat format) {
+		int width;
+		if(format == StringFormat.GCG || format == StringFormat.MSF) {
+			width = 50;
+		} else {
+			width = 60;
+		}
+		return toString(format, width);
+	}
 
 	@Override
 	public String toString() {

biojava-core/src/main/java/org/biojava/nbio/core/alignment/template/Profile.java

@@ -116,6 +116,7 @@ enum StringFormat {
 		 *<div class="subText">          <b>Legend:</b>          <span style="color:green">Green</span> - identical residues |          <span style="color:pink">Pink</span> - similar residues |           <span style="color:blue">Blue</span> - sequence mismatch |          <span style="color:brown">Brown</span> - insertion/deletion |      </div>
 		 */
 		PDBWEB,
+		CONCENSUS,
 	}
 
 	/**
@@ -341,4 +342,13 @@ enum StringFormat {
 	 */
 	String toString(StringFormat format);
 
+	/**
+	 * Returns a formatted view of the alignment profile.  Details depend on the format given.
+	 *
+	 * @param format output format
+	 * @param width limit on the line length
+	 * @return a formatted view of the alignment profile
+	 */
+	String toString(StringFormat format, int width);
+
 }

biojava-core/src/main/java/org/biojava/nbio/core/sequence/MultipleSequenceAlignment.java

@@ -28,6 +28,8 @@
 import org.biojava.nbio.core.sequence.template.CompoundSet;
 import org.biojava.nbio.core.sequence.template.LightweightProfile;
 import org.biojava.nbio.core.sequence.template.Sequence;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
 
 import java.util.ArrayList;
 import java.util.Collections;
@@ -41,6 +43,7 @@
  * @author Mark Chapman
  */
 public class MultipleSequenceAlignment<S extends Sequence<C>, C extends Compound> implements LightweightProfile<S, C> {
+	private static Logger logger = LoggerFactory.getLogger(MultipleSequenceAlignment.class);
 
 	private List<S> sequences = new ArrayList<S>();
 	private Integer length = null;
@@ -149,22 +152,37 @@ public String toString(int width) {
 	 * @return String in one of the supported file formats.
 	 */
 	@Override
-	public String toString(StringFormat format) {
+	public String toString(StringFormat format, int width) {
 		switch (format) {
+		default:
+			logger.warn("Unrecognized StringFormat {}", format);
+			// fall through
 		case ALN:
 		case CLUSTALW:
-		default:
-			return toString(60, String.format("CLUSTAL W MSA from BioJava%n%n"), IOUtils.getIDFormat(sequences) +
+			return toString(width, String.format("CLUSTAL W MSA from BioJava%n%n"), IOUtils.getIDFormat(sequences) +
 					"   ", true, false, true, false);
 		case FASTA:
-			return toString(60, null, ">%s%n", false, false, false, false);
+			return toString(width, null, ">%s%n", false, false, false, false);
 		case GCG:
 		case MSF:
-			return toString(50, IOUtils.getGCGHeader(sequences), IOUtils.getIDFormat(sequences), true, false, false,
+			return toString(width, IOUtils.getGCGHeader(sequences), IOUtils.getIDFormat(sequences), true, false, false,
 					false);
 		case PDBWEB:
-			return toString(60, null, "%s", true, false, true, true);
+			return toString(width, null, "%s", true, false, true, true);
+		case CONCENSUS:
+			return toString(width, null, null, true, false, true, false);
+		}
+	}
+
+	@Override
+	public String toString(StringFormat format) {
+		int width;
+		if(format == StringFormat.GCG || format == StringFormat.MSF) {
+			width = 50;
+		} else {
+			width = 60;
 		}
+		return toString(format, width);
 	}
 
 	/**

biojava-core/src/main/java/org/biojava/nbio/core/sequence/template/LightweightProfile.java

@@ -44,7 +44,8 @@ enum StringFormat {
 		FASTA,
 		GCG,
 		MSF,
-		PDBWEB
+		PDBWEB,
+		CONCENSUS,
 	}
 
 	/**
@@ -121,4 +122,12 @@ enum StringFormat {
 	 */
 	String toString(StringFormat format);
 
+	/**
+	 * Returns a formatted view of the alignment profile.  Details depend on the format given.
+	 *
+	 * @param format output format
+	 * @param width limit on the line length
+	 * @return a formatted view of the alignment profile
+	 */
+	String toString(StringFormat format, int width);
 }

biojava-core/src/test/resources/org/biojava/nbio/core/alignment/SimpleProfileTest.CONCENSUS

@@ -0,0 +1,3 @@
+ARND- 4
+ | | 
+-R-DG 3

biojava-core/src/test/resources/org/biojava/nbio/core/sequence/MultipleSequenceAlignmentTest.CONCENSUS

@@ -0,0 +1,8 @@
+ARNDCEQGHILKMFPSTWYVBZJX
+ARNDCEQGHILKMFPSTWYVBZJX
+ARNDCEQGHILKMFPSTWYVBZJX
+ARNDCEQGHILKMFPSTWYVBZJX
+ARNDCEQGHILKMFPSTWYVBZJX
+ARNDCEQGHILKMFPSTWYVBZJX
+ARNDCEQGHILKMFPSTWYVBZJX
+ARNDCEQGHILKMFPSTWYVBZJX