Revision: 21207
http://sourceforge.net/p/jmol/code/21207
Author: hansonr
Date: 2016-08-10 21:51:12 +0000 (Wed, 10 Aug 2016)
Log Message:
-----------
even simpler mmtf decoding
Modified Paths:
--------------
branches/v14_6/Jmol/src/org/jmol/adapter/readers/cif/MessagePackReader.java
trunk/Jmol/src/org/jmol/adapter/readers/cif/MessagePackReader.java
Modified:
branches/v14_6/Jmol/src/org/jmol/adapter/readers/cif/MessagePackReader.java
===================================================================
--- branches/v14_6/Jmol/src/org/jmol/adapter/readers/cif/MessagePackReader.java
2016-08-10 17:34:01 UTC (rev 21206)
+++ branches/v14_6/Jmol/src/org/jmol/adapter/readers/cif/MessagePackReader.java
2016-08-10 21:51:12 UTC (rev 21207)
@@ -328,11 +328,11 @@
int param = BC.bytesToInt(b, 8, true);
switch (type) {
case 1:
- return getFloats(b, 4, 1);
+ return getFloats(b, n, 1);
case 2: // 1-byte
case 3: // 2-byte
case 4: // 4-byte
- return getInts(b, 1 << (type - 2));
+ return getInts(b, n);
case 5:
return rldecode32ToStr(b);
case 6:
@@ -346,7 +346,7 @@
case 10:
return unpack16Deltaf(b, n, param);
case 11:
- return getFloats(b, 2, param);
+ return getFloats(b, n, param);
case 12: // two-byte
case 13: // one-byte
return unpackf(b, 14 - type, n, param);
@@ -372,16 +372,15 @@
public static float[] getFloats(byte[] b, int n, float divisor) {
if (b == null)
return null;
- int len = (b.length - 12) / n;
- float[] a = new float[len];
+ float[] a = new float[n];
try {
- switch (n) {
+ switch ((b.length - 12) / n) {
case 2:
- for (int i = 0, j = 12; i < len; i++, j += 2)
+ for (int i = 0, j = 12; i < n; i++, j += 2)
a[i] = BC.bytesToShort(b, j, false) / divisor;
break;
case 4:
- for (int i = 0, j = 12; i < len; i++, j += 4)
+ for (int i = 0, j = 12; i < n; i++, j += 4)
a[i] = BC.bytesToFloat(b, j, false);
break;
}
@@ -396,27 +395,25 @@
* Decode a byte array into a byte, short, or int array.
*
* @param b
- * @param nbytes
- * 1 (byte), 2 (int16), or 4 (int32)
+ * @param n
*
* @return array of integers
*/
- public static int[] getInts(byte[] b, int nbytes) {
+ public static int[] getInts(byte[] b, int n) {
if (b == null)
return null;
- int len = (b.length - 12) / nbytes;
- int[] a = new int[len];
- switch (nbytes) {
+ int[] a = new int[n];
+ switch ((b.length - 12) / n) {
case 1:
- for (int i = 0, j = 12; i < len; i++, j++)
+ for (int i = 0, j = 12; i < n; i++, j++)
a[i] = b[j];
break;
case 2:
- for (int i = 0, j = 12; i < len; i++, j += 2)
+ for (int i = 0, j = 12; i < n; i++, j += 2)
a[i] = BC.bytesToShort(b, j, true);
break;
case 4:
- for (int i = 0, j = 12; i < len; i++, j += 4)
+ for (int i = 0, j = 12; i < n; i++, j += 4)
a[i] = BC.bytesToInt(b, j, true);
break;
}
@@ -520,7 +517,8 @@
/**
* mmtf type 9
*
- * Decode an array of int32 using run-length decoding.
+ * Decode an array of int32 using run-length decoding and divide by a divisor
+ * to give a float32.
*
* @param b
* @param n
Modified: trunk/Jmol/src/org/jmol/adapter/readers/cif/MessagePackReader.java
===================================================================
--- trunk/Jmol/src/org/jmol/adapter/readers/cif/MessagePackReader.java
2016-08-10 17:34:01 UTC (rev 21206)
+++ trunk/Jmol/src/org/jmol/adapter/readers/cif/MessagePackReader.java
2016-08-10 21:51:12 UTC (rev 21207)
@@ -328,11 +328,11 @@
int param = BC.bytesToInt(b, 8, true);
switch (type) {
case 1:
- return getFloats(b, 4, 1);
+ return getFloats(b, n, 1);
case 2: // 1-byte
case 3: // 2-byte
case 4: // 4-byte
- return getInts(b, 1 << (type - 2));
+ return getInts(b, n);
case 5:
return rldecode32ToStr(b);
case 6:
@@ -346,7 +346,7 @@
case 10:
return unpack16Deltaf(b, n, param);
case 11:
- return getFloats(b, 2, param);
+ return getFloats(b, n, param);
case 12: // two-byte
case 13: // one-byte
return unpackf(b, 14 - type, n, param);
@@ -372,16 +372,15 @@
public static float[] getFloats(byte[] b, int n, float divisor) {
if (b == null)
return null;
- int len = (b.length - 12) / n;
- float[] a = new float[len];
+ float[] a = new float[n];
try {
- switch (n) {
+ switch ((b.length - 12) / n) {
case 2:
- for (int i = 0, j = 12; i < len; i++, j += 2)
+ for (int i = 0, j = 12; i < n; i++, j += 2)
a[i] = BC.bytesToShort(b, j, false) / divisor;
break;
case 4:
- for (int i = 0, j = 12; i < len; i++, j += 4)
+ for (int i = 0, j = 12; i < n; i++, j += 4)
a[i] = BC.bytesToFloat(b, j, false);
break;
}
@@ -396,27 +395,25 @@
* Decode a byte array into a byte, short, or int array.
*
* @param b
- * @param nbytes
- * 1 (byte), 2 (int16), or 4 (int32)
+ * @param n
*
* @return array of integers
*/
- public static int[] getInts(byte[] b, int nbytes) {
+ public static int[] getInts(byte[] b, int n) {
if (b == null)
return null;
- int len = (b.length - 12) / nbytes;
- int[] a = new int[len];
- switch (nbytes) {
+ int[] a = new int[n];
+ switch ((b.length - 12) / n) {
case 1:
- for (int i = 0, j = 12; i < len; i++, j++)
+ for (int i = 0, j = 12; i < n; i++, j++)
a[i] = b[j];
break;
case 2:
- for (int i = 0, j = 12; i < len; i++, j += 2)
+ for (int i = 0, j = 12; i < n; i++, j += 2)
a[i] = BC.bytesToShort(b, j, true);
break;
case 4:
- for (int i = 0, j = 12; i < len; i++, j += 4)
+ for (int i = 0, j = 12; i < n; i++, j += 4)
a[i] = BC.bytesToInt(b, j, true);
break;
}
@@ -520,7 +517,8 @@
/**
* mmtf type 9
*
- * Decode an array of int32 using run-length decoding.
+ * Decode an array of int32 using run-length decoding and divide by a divisor
+ * to give a float32.
*
* @param b
* @param n
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