biojava
diff --git a/‎biojava-core/src/main/java/org/biojava/nbio/core/alignment/template/AlignedSequence.java‎
Lines changed: 16 additions & 0 deletions b/‎biojava-core/src/main/java/org/biojava/nbio/core/alignment/template/AlignedSequence.java‎
Lines changed: 16 additions & 0 deletions
diff --git a/‎biojava-structure/src/main/java/org/biojava/nbio/structure/cath/CathInstallation.java‎
Lines changed: 2 additions & 1 deletion b/‎biojava-structure/src/main/java/org/biojava/nbio/structure/cath/CathInstallation.java‎
Lines changed: 2 additions & 1 deletion
@@ -158,4 +158,20 @@ enum Step { COMPOUND, GAP }
 	 */
 	boolean isGap(int alignmentIndex);
 
+	/**
+	 * Returns number of gap positions (gap openings and extensions) in the sequence. This could be determined from the {@link Location}
+	 * information or from gap {@link Compound}s, which may not necessarily result in the same number.
+	 *
+	 * @return number of gap positions in the sequence
+	 */
+	int getNumGapPositions();
+
+	/**
+	 * Returns the coverage, as a fraction between 0 and 1, of this {@link AlignedSequence} with respect to the original sequence.
+	 * This is equivalent to ({@link #getLength()} - {@link #getNumGapPositions()}) / getOriginalSequence().getLength().
+	 *
+	 * @return coverage of the original sequence by the aligned sequence
+	 */
+	double getCoverage();
+
 }
@@ -636,6 +636,7 @@ private void parseCathDomall(BufferedReader bufferedReader) throws IOException{
 
 	protected void downloadFileFromRemote(URL remoteURL, File localFile) throws IOException{
 //        System.out.println("downloading " + remoteURL + " to: " + localFile);
+		LOGGER.info("Downloaded file {} to local file {}", remoteURL, localFile);
 
 		long timeS = System.currentTimeMillis();
 		File tempFile  = File.createTempFile(FileDownloadUtils.getFilePrefix(localFile), "."+ FileDownloadUtils.getFileExtension(localFile));
@@ -665,7 +666,7 @@ protected void downloadFileFromRemote(URL remoteURL, File localFile) throws IOEx
 			disp = disp / 1024.0;
 		}
 		long timeE = System.currentTimeMillis();
-		LOGGER.info("Downloaded file {} ({}) to local file {} in {} sec.", remoteURL, String.format("%.1f",disp) + unit, localFile, (timeE - timeS)/1000);
+		LOGGER.info("Downloaded {} in {} sec. to {}", String.format("%.1f",disp) + unit, (timeE - timeS)/1000, localFile);
 	}
 
 	private boolean domainDescriptionFileAvailable(){
Original file line number	Diff line number	Diff line change
`@@ -636,6 +636,7 @@ private void parseCathDomall(BufferedReader bufferedReader) throws IOException{`
`636`	`636`
`637`	`637`	`protected void downloadFileFromRemote(URL remoteURL, File localFile) throws IOException{`
`638`	`638`	`// System.out.println("downloading " + remoteURL + " to: " + localFile);`
	`639`	`+ LOGGER.info("Downloaded file {} to local file {}", remoteURL, localFile);`
`639`	`640`
`640`	`641`	`long timeS = System.currentTimeMillis();`
`641`	`642`	`File tempFile = File.createTempFile(FileDownloadUtils.getFilePrefix(localFile), "."+ FileDownloadUtils.getFileExtension(localFile));`
`@@ -665,7 +666,7 @@ protected void downloadFileFromRemote(URL remoteURL, File localFile) throws IOEx`
`665`	`666`	`disp = disp / 1024.0;`
`666`	`667`	`}`
`667`	`668`	`long timeE = System.currentTimeMillis();`
`668`		`- LOGGER.info("Downloaded file {} ({}) to local file {} in {} sec.", remoteURL, String.format("%.1f",disp) + unit, localFile, (timeE - timeS)/1000);`
	`669`	`+ LOGGER.info("Downloaded {} in {} sec. to {}", String.format("%.1f",disp) + unit, (timeE - timeS)/1000, localFile);`
`669`	`670`	`}`
`670`	`671`
`671`	`672`	`private boolean domainDescriptionFileAvailable(){`